Some of his early novels, called "scientific romances", invented several themes now classic in science fiction in such works as The Time Machine, The Island of Doctor Moreau, The Invisible Man, The War of the Worlds, When the Sleeper Wakes, and The First Men in the Moon. He also wrote realistic novels that received critical acclaim, including Kipps and a critique of English culture during the Edwardian period, Tono-Bungay. Wells also wrote dozens of short stories and novellas, including, "The Flowering of the Strange Orchid", which helped bring the full impact of Darwin's revolutionary botanical ideas to a wider public, and was followed by many later successes such as "The Country of the Blind" (1904).

According to James Gunn, one of Wells's major contributions to the science fiction genre was his approach, which he referred to as his "new system of ideas". In his opinion, the author should always strive to make the story as credible as possible, even if both the writer and the reader knew certain elements are impossible, allowing the reader to accept the ideas as something that could really happen, today referred to as "the plausible impossible" and "suspension of disbelief". While neither invisibility nor time travel was new in speculative fiction, Wells added a sense of realism to the concepts which the readers were not familiar with. He conceived the idea of using a vehicle that allows an operator to travel purposely and selectively forwards or backwards in time. The term "time machine", coined by Wells, is now almost universally used to refer to such a vehicle. He explained that while writing The Time Machine, he realised that "the more impossible the story I had to tell, the more ordinary must be the setting, and the circumstances in which I now set the Time Traveller were all that I could imagine of solid upper-class comforts". In "Wells's Law", a science fiction story should contain only a single extraordinary assumption. Being aware the notion of magic as something real had disappeared from society, he, therefore, used scientific ideas and theories as a substitute for magic to justify the impossible. Wells's best-known statement of the "law" appears in his introduction to a collection of his works published in 1934:

As soon as the magic trick has been done the whole business of the fantasy writer is to keep everything else human and real. Touches of prosaic detail are imperative and a rigorous adherence to the hypothesis. Any extra fantasy outside the cardinal assumption immediately gives a touch of irresponsible silliness to the invention.

Dr. Griffin / The Invisible Man is a brilliant research scientist who discovers a method of invisibility, but finds himself unable to reverse the process. An enthusiast of random and irresponsible violence, Griffin has become an iconic character in horror fiction. The Island of Doctor Moreau sees a shipwrecked man left on the island home of Doctor Moreau, a mad scientist who creates human-like hybrid beings from animals via vivisection. The earliest depiction of uplift, the novel deals with a number of philosophical themes, including pain and cruelty, moral responsibility, human identity, and human interference with nature. Though Tono-Bungay is not a science-fiction novel, radioactive decay plays a small but consequential role in it. Radioactive decay plays a much larger role in The World Set Free (1914). This book contains what is surely his biggest prophetic "hit", with the first description of a nuclear weapon. Scientists of the day were well aware that the natural decay of radium releases energy at a slow rate over thousands of years. The rate of release is too slow to have practical utility, but the total amount released is huge. Wells's novel revolves around an (unspecified) invention that accelerates the process of radioactive decay, producing bombs that explode with no more than the force of ordinary high explosives—but which "continue to explode" for days on end. "Nothing could have been more obvious to the people of the earlier twentieth century", he wrote, "than the rapidity with which war was becoming impossible ... [but] they did not see it until the atomic bombs burst in their fumbling hands". In 1932, the physicist and conceiver of nuclear chain reaction Leó Szilárd read The World Set Free (the same year Sir James Chadwick discovered the neutron), a book which he said made a great impression on him.

Wells also wrote non-fiction. His first non-fiction bestseller was Anticipations of the Reaction of Mechanical and Scientific Progress upon Human Life and Thought (1901). When originally serialised in a magazine it was subtitled "An Experiment in Prophecy", and is considered his most explicitly futuristic work. It offered the immediate political message of the privileged sections of society continuing to bar capable men from other classes from advancement until war would force a need to employ those most able, rather than the traditional upper classes, as leaders. Anticipating what the world would be like in the year 2000, the book is interesting both for its hits (trains and cars resulting in the dispersion of populations from cities to suburbs; moral restrictions declining as men and women seek greater sexual freedom; the defeat of German militarism, and the existence of a European Union) and its misses (he did not expect successful aircraft before 1950, and averred that "my imagination refuses to see any sort of submarine doing anything but suffocate its crew and founder at sea").

His bestselling two-volume work, The Outline of History (1920), began a new era of popularised world history. It received a mixed critical response from professional historians. However, it was very popular amongst the general population and made Wells a rich man. Many other authors followed with "Outlines" of their own in other subjects. He reprised his Outline in 1922 with a much shorter popular work, A Short History of the World, a history book praised by Albert Einstein, and two long efforts, The Science of Life (1930)—written with his son G. P. Wells and evolutionary biologist Julian Huxley, and The Work, Wealth and Happiness of Mankind (1931). The "Outlines" became sufficiently common for James Thurber to parody the trend in his humorous essay, "An Outline of Scientists"—indeed, Wells's Outline of History remains in print with a new 2005 edition, while A Short History of the World has been re-edited (2006).

From quite early in Wells's career, he sought a better way to organise society and wrote a number of Utopian novels. The first of these was A Modern Utopia (1905), which shows a worldwide utopia with "no imports but meteorites, and no exports at all"; two travellers from our world fall into its alternate history. The others usually begin with the world rushing to catastrophe, until people realise a better way of living: whether by mysterious gases from a comet causing people to behave rationally and abandoning a European war (In the Days of the Comet (1906)), or a world council of scientists taking over, as in The Shape of Things to Come (1933, which he later adapted for the 1936 Alexander Korda film, Things to Come). This depicted, all too accurately, the impending World War, with cities being destroyed by aerial bombs. He also portrayed the rise of fascist dictators in The Autocracy of Mr Parham (1930) and The Holy Terror (1939). Men Like Gods (1923) is also a utopian novel. Wells in this period was regarded as an enormously influential figure; the critic Malcolm Cowley stated: "by the time he was forty, his influence was wider than any other living English writer".

Wells contemplates the ideas of nature and nurture and questions humanity in books such as The Island of Doctor Moreau. Not all his scientific romances ended in a Utopia, and Wells also wrote a dystopian novel, When the Sleeper Wakes (1899, rewritten as The Sleeper Awakes, 1910), which pictures a future society where the classes have become more and more separated, leading to a revolt of the masses against the rulers. The Island of Doctor Moreau is even darker. The narrator, having been trapped on an island of animals vivisected (unsuccessfully) into human beings, eventually returns to England; like Gulliver on his return from the Houyhnhnms, he finds himself unable to shake off the perceptions of his fellow humans as barely civilised beasts, slowly reverting to their animal natures.

Wells also wrote the preface for the first edition of W. N. P. Barbellion's diaries, The Journal of a Disappointed Man, published in 1919. Since "Barbellion" was the real author's pen name, many reviewers believed Wells to have been the true author of the Journal; Wells always denied this, despite being full of praise for the diaries.