On December 26, 1856, Gibson purchased a place in the South bank of River Min and established there in 1859 a commodious wooden Western-style boarding school for laymen and ministers.

[2][4][5] On June 14, 1857, Otis Gibson and Robert S. Maclay baptized their first convert, a native tradesman named Ting Ang (陈安).

[2] Due to his wife Eliza's failing health, Otis Gibson left China with her in 1865 and returned to Moira, New York as a pastor.

Gibson had erected the building of the "Chinese Mission Institute" on Washington Street in San Francisco's Chinatown.

[1][9][10][11] In his later life, Otis Gibson made untiring and courageous efforts in behalf of the poor and the wronged of the Chinese on the Pacific Coast.

[12] In his landmark work The Chinese in America (唐人在金山, ISBN 0-405-11272-6) which was published in 1877, Gibson concluded his polemic against the anti-Chinese arguments with a noble restatement of the American ideal: The doors of our country are open equally... We have room for all.

The oppressed and down-trodden from all nations may alike find shelter here, and under the benign influences of our free institutions, and of our exalted faith, with the blessing of Almighty God, these different nationalities and varying civilizations shall, in time, blend into one harmonious whole, illustrating to a wondering world the common Fatherhood of God, and the universal brotherhood of man.Otis Gibson was strongly anti-Catholic.

The great 1906 earthquake and fire destroyed Gibson's Washington Street building that housed the Chinese Mission, along with most of San Francisco Chinatown.

In 1911, after five years of displacement and fund raising,[18] the Chinese Methodist Church was rebuilt on the corner of Washington and Stockton Streets.