Willis was born in London, the son of a North London builder, and with George Cooper, later sub-organist of St Paul's Cathedral, he learned to play the organ with some help from Thomas Attwood, St Paul's organist. In 1835, Willis was articled to organ builder John Gray (later Gray and Davison) for seven years. During this time, he invented the manual and pedal couplers which he used throughout his later career. He also became organist of Christ Church Hoxton, the first of a series of organist posts; Christ Church, Hampstead from 1852 to 1859, where he had built the organ; and then the Chapel-of-Ease, Islington (now St Mary Magdalene Church) for nearly thirty years. He was renowned for always arranging his business trips so he could return by Sunday to play for the service.
Following his apprenticeship he worked for three years in Cheltenham, assisting an instrument maker, W.E. Evans, who specialised in free reed instruments. Willis later attributed his personal skill in reed voicing to this experience. Willis met Samuel Sebastian Wesley at Cheltenham, and this led to the re-building of the Gloucester Cathedral organ in 1847. Willis had become an independent organ builder and commented, "It was my stepping stone to fame... I received £400 for the job, and was presumptuous enough to marry."
He was born to Henry Willis (1792–1872) and Elizabeth. He married Esther Maria Chatterton on 7 April 1847 in St Andrew's Church, Holborn and they had the following childrenVincent Willis (1848 – 1928)
Edith Willis (1850 – 1947)
Henry Willis II (1852 – 1927)
Kate Willis (1853 – 1927)
Mary Willis (1859 – 1952)
Esther died in 1893 and on 7 August 1894 he married Rosetta Chatterton (1831–1912) at St Thomas' Church, Camden Town.
For the Great Exhibition of 1851, Willis erected the largest of the organs exhibited with an unprecedented 70 speaking stops. He introduced several novel features, which had a significant effect on organ design. Piston buttons were inserted between the manuals to allow automatic selection of blocks of "stops", and Barker lever servo action was used on the manuals to overcome the constraints of tracker action connecting rods for an instrument of such size and complexity. After the exhibition ended, the instrument was erected in reduced form at Winchester Cathedral where in 1854 it now had 49 speaking stops over four manuals and pedals, and the first concave and radiating pedalboard. The pedalboard was the joint idea of Willis and Samuel Sebastian Wesley with whom Willis collaborated on his next large organ of 100 speaking stops at St George's Hall, Liverpool in 1855.
The Exhibition organ had led to the contract for St George's Hall, Liverpool, where the virtuosic playing of W.T. Best drew large crowds, and also spread the fame of Willis as a builder still further. In a long career stretching to the end of the 19th century, Willis subsequently built the organs at the Alexandra Palace, the Royal Albert Hall, and St Paul's Cathedral. Among the approximately 1,000 organs that he built or re-built were the cathedral instruments at Canterbury, Carlisle, Coventry, Durham, Edinburgh (St Mary's Episcopal Cathedral), Exeter, Glasgow (The High Kirk of Glasgow), Gloucester, Hereford, Lincoln, St Davids Cathedral Pembrokeshire, St Paul's Cathedral London, Salisbury, Truro, Wells and Winchester. In addition there were a large number of concert and parish church organs of note, including the organ at St George's Hall Windsor Castle, sadly destroyed by fire in 1992. The last major instrument which he personally supervised was at St Bees Priory in 1899, which he voiced himself, although approaching his 80th year.
Willis died in London in 1901. His instruments can be found across the world, particularly in the former British Empire, and his superb reed voicing and excellent mechanical craftmanship can still be experienced on many instruments today.
Four generations of the Willis family continued the family tradition of organ building until 1997, when Henry Willis IV retired and the first non-family Managing Director was appointed. On 28 November 1998 the total shareholding of the Willis family was acquired. The Company, founded in 1845, Henry Willis & Sons, Ltd. still makes organs in Liverpool.