He married Elizabeth Anna Maria Wathen (1807-1867), the second daughter of Nathaniel Wathen, a wealthy clothier of Stroud, Gloucestershire on 25 January 1831 at St. Pancras Church in Camden, London. They had five children. Thompson died of bronchitis at the age of 52 on 11 Aug. 1860 in Sutton, Surrey, and is buried in Norwood Cemetery in Lambeth, London. There is a watercolor portrait of him that was painted by the artist Alfred Essex (d. 1871), as well as a miniature portrait by Alfred's brother, William Essex (1784?-1869). There is also a photograph of Theophilus Thompson in the National Portrait Gallery in London. He authored several papers, including the following. In addition to Thompson's academic pursuits, he also acted as the London literary agent for his brother-in-law George Henry Wathen, who was editor of an Australian periodical called the "Australasian," and author of a book on Egyptian antiquities, and another on gold mining in Australia. There in fact exists a letter between Thompson and Charles Dickens discussing the merits of the "Australasian."