died at Whaddon Hall on 5 Feb. 1760, and was buried beneath the altar in Fenny Stratford chapel on 11 Feb., where there is an inscription to his memory. His wife died at Whaddon Hall on 2 Oct. 1724, aged 34, and was buried under a raised table-tomb at Bletchley. Of their ten children, eight were alive in 1724, but only the twin-daughters Gertrude and Catherine survived in 1760, and they both died in 1772. His grandson took the name of Fleming and lived at Stoneham. Willis appointed his eldest grandson and heir the sole executor, and left him all his books and pictures, except Rymer's ‘Fœdera,’ which he gave to Trinity College, Oxford, and the choice of one book to the Rev. Francis Wise [q. v.] His manuscripts were to go within three months to the Bodleian Library. They consisted of fifty-nine folio, forty-eight quarto, and five octavo volumes, of much value for ecclesiastical topography and biography, the history of Buckinghamshire and that of the four Welsh cathedrals. He left to Oxford University his ‘numerous silver, brass, copper, and pewter coins, also his gold coins, if purchased at the rate of 4l. per ounce,’ which was at once done. In 1720 he gave to that library ten valuable manuscripts and his grandfather's portrait, and between 1739 and 1750 he had given other coins. Many of his letters are among the Ballard and Rawlinson manuscripts (Macray, Bodleian Libr. pp. 221, 259–60, 483–4; Madan, Western MSS. iii. 578, 602). Large collections of letters and papers by or relating to him are in the British Museum, especially among the Cole manuscripts. Willis's benefactions included the revival in 1702 of the market at Fenny Stratford, a hamlet contiguous to Bletchley, and the raising, in concurrence with his cousin Dr. Martin Benson (afterwards bishop of Gloucester), of money for building there between 1724 and 1730 the chapel of St. Martin. It was a memorial of his grandfather, whose portrait was placed over the entrance, and, as he died on St. Martin's day 1675, Willis left a benefaction for a sermon in the chapel every year on that day. He contributed materially towards the rebuilding of part of Stony Stratford church in 1746; in 1752 he gave 200l. for the repairs of Buckingham church, and in 1756 he restored Bow Brickhill church, which had been disused for nearly 150 years. The chancel of the church at Little Brickhill was repaired through his liberality, and he erected at the cathedral at Christ Church, Oxford, a monument for Canon Iles, who had helped his grandfather at the university. The celebration at Fenny Stratford of St. Martin's day, regularly maintained by Willis during his life, is still observed by its inhabitants.
The foibles and appearance of Willis were satirised in lines written by Dr. Darrell of Lillingston-Darrell. They were printed in the ‘Oxford Sausage’ and, with Cole's notes ‘when out of humour with him,’ in ‘Notes and Queries’ (2nd ser. vi. 428–9). A sarcastic description of his house is in Nichols's ‘Illustrations of Literature’ (i. 682–4). Hearne wrote ‘An Account of my Journey to Whaddon Hall, 1716,’ which is printed in ‘Letters from the Bodleian Library’ (ii. 175–83).
Willis's portrait was etched in 1781 at Cole's request from a drawing made by Rev. Michael Tyson of the original painting by Dahl. It is reproduced in Nichols's ‘Literary Anecdotes’ (viii. 219) and Hutchins's ‘Dorset’ (2nd ed. iv. 335). Portraits of his father, mother, and other members of the family were at Bletchley.
Among the literary works of Willis are included surveys of the four Welsh cathedrals, viz. St. David's (1717), Llandaff (1719), St. Asaph (1720), and Bangor (1721); but the description of St. David's is signed ‘M. N.,’ and was drawn up by Dr. William Wotton (the initials being the concluding letters of his names), and that of Llandaff, which was also compiled by Wotton, has his name in full. Willis published in 1727 two volumes of ‘A Survey of the Cathedrals of York, Durham, Carlisle, Chester, Man, Lichfield, Hereford, Worcester, Gloucester and Bristol,’ and he issued in 1730 a third volume on ‘Lincoln, Ely, Oxford, and Peterborough.’ Thomas Osborne, the bookseller, purchased the unsold copies of this impression and advertised his issue in 1742 as a new edition containing histories of all the cathedrals, whereupon Willis denounced the proceeding in the ‘London Evening Post,’ 5–8 March 1743. The volumes of the 1742 issue at the British Museum have copious notes by William Cole [q. v.], and transcripts of Willis's additions in his own copy. One impression at the British Museum of the volume on Llandaff Cathedral has many notes by Gough, and an edition of the survey of St. Asaph, enlarged and brought down to date, was published in 1801. The account of the ‘Cathedral of Man’ is reproduced in Harrison's ‘Old Historians’ of that isle (Manx Soc. xviii. 126–51), the survey of Lincoln Cathedral formed the basis of a volume on ‘The Antiquities in Lincoln Cathedral’ (1771), and a ‘History of Gothic and Saxon Architecture in England’ (1798) was compiled from his works and those of James Bentham [q. v.]