He has written books and articles on numerous topics in the history of sixteenth, seventeenth, and eighteenth century science including books on the work of Francis Bacon, the Scientific Revolution, and Nicolaus Copernicus. His articles include research on the work of Isaac Newton and later Newtonianism, Atomism and a range of other subjects. Often his focus is on the unexpected links between the development of modern science and previous systems of knowledge and understanding, particularly those of Natural Magic. In this respect his work can be seen to disagree with The Zilsel Thesis which sees the emergence of modern Science as being a radical break with the previous religious or magical traditions. Instead of seeing a great rift, John Henry's work emphasises the importance of investigative techniques taken from magical traditions for many of the key figures of the scientific revolution.