The following are some of the more important of his works:
* 1660 – New Experiments Physico-Mechanical: Touching the Spring of the Air and their Effects
* 1661 – The Sceptical Chymist
* 1662 – Whereunto is Added a Defence of the Authors Explication of the Experiments, Against the Obiections of Franciscus Linus and Thomas Hobbes (a book-length addendum to the second edition of New Experiments Physico-Mechanical)
* 1663 – Considerations touching the Usefulness of Experimental Natural Philosophy (followed by a second part in 1671)
* 1664 – Experiments and Considerations Touching Colours, with Observations on a Diamond that Shines in the Dark
* 1665 – New Experiments and Observations upon Cold
* 1666 – Hydrostatical Paradoxes
* 1666 – Origin of Forms and Qualities according to the Corpuscular Philosophy. (A continuation of his work on the spring of air demonstrated that a reduction in ambient pressure could lead to bubble formation in living tissue. This description of a viper in a vacuum was the first recorded description of decompression sickness.)
* 1669 – A Continuation of New Experiments Physico-mechanical, Touching the Spring and Weight of the Air, and Their Effects
* 1670 – Tracts about the Cosmical Qualities of Things, the Temperature of the Subterraneal and Submarine Regions, the Bottom of the Sea, &tc. with an Introduction to the History of Particular Qualities
* 1672 – Origin and Virtues of Gems
* 1673 – Essays of the Strange Subtilty, Great Efficacy, Determinate Nature of Effluviums
* 1674 – Two volumes of tracts on the Saltiness of the Sea, Suspicions about the Hidden Realities of the Air, Cold, Celestial Magnets 
* 1674 – Animadversions upon Mr. Hobbess Problemata de Vacuo'
* 1676 – Experiments and Notes about the Mechanical Origin or Production of Particular Qualities, including some notes on electricity and magnetism
* 1678 – Observations upon an artificial Substance that Shines without any Preceding Illustration
* 1680 – The Aerial Noctiluca
* 1682 – New Experiments and Observations upon the Icy Noctiluca (a further continuation of his work on the air)
* 1684 – Memoirs for the Natural History of the Human Blood
* 1685 – Short Memoirs for the Natural Experimental History of Mineral Waters
* 1686 – A Free Enquiry into the Vulgarly Received Notion of Nature
* 1690 – Medicina Hydrostatica
* 1691 – Experimenta et Observationes Physicae
Among his religious and philosophical writings were:
* 1648 (1659) – Some Motives and Incentives to the Love of God, often known by its running head Seraphic Love, written in 1648, but not published until 1659
* 1663 – Some Considerations Touching the Style of the H[oly] Scriptures
* 1664 – Excellence of Theology compared with Natural Philosophy
* 1665 – Occasional Reflections upon Several Subjects, which was ridiculed by Swift in Meditation Upon a Broomstick, and by Butler in An Occasional Reflection on Dr Charltons Feeling a Dogs Pulse at Gresham College
* 1675 – Some Considerations about the Reconcileableness of Reason and Religion, with a Discourse about the Possibility of the Resurrection
* 1687 – The Martyrdom of Theodora, and of Didymus
* 1690 – The Christian Virtuoso