 Thompson was also involved in music, writing books on Harmony and Just Intonation e.g.for the guitar ("Instructions to my daughter for playing on the enharmonic guitar"), and building an organ with over 40 notes to the octave, to "realise the visions of Guido and Mersenne.Monuments to his second son General Charles William Thompson, his youngest son Lieutenant Colonel John Wycliffe Thompson, who served in the Crimean War, and his youngest daughter Anne Elise are in the chancel of St Mary's Church, Cottingham, near Hull.