Williams was born in Utica, New York and studied at Rensselaer Polytechnic Institute in Troy, New York. On graduation he was elected as a Professor of the Institute.
On the June 15 1833, and still in his twenties, he sailed for China to take charge of the printing press of the American Board of Commissioners for Foreign Missions at Guangdong, China. In 1837 he sailed on the to Japan. Officially this trip was to return some stranded Japanese sailors, but it was also an unsuccessful attempt to open Japan to American trade.
On November 20 1845 Williams married Sarah Walworth. From 1848 to 1851 Williams was the editor of the Chinese Repository, a leading Western journal published in China. In 1853 he was attached to Commodore Matthew Calbraith Perry's expedition to Japan as an official interpreter.
In 1855, Williams was appointed Secretary of the United States Legation to China. During his stay in China, he wrote ''A Tonic Dictionary Of The Chinese Language In The Canton Dialect'' in 1856. After years of opposition from the , Williams was instrumental in the negotiation of the Treaty of Tientsin, which provided for the toleration of both Chinese and foreign Christians.
In 1860, he was appointed chargé d'affaires for the United States in Beijing. He resigned his position on October 25 1876, 43 years to the day that he first landed at Guangzhou in 1833. Around 1875, he completed a translation of the Book of Genesis and the Gospel of Matthew into , but the manuscripts were lost in a fire before they could be published.
He returned to the United States in 1877 and became the first Professor of Chinese language and Chinese literature in the United States at Yale University. Williams was nominated as president of the American Bible Society on February 3, 1881. He died on February 16, 1884.
*''The Chinese commercial guide''
*''A Tonic Dictionary Of The Chinese Language In The Canton Dialect''
*''The Middle Kingdom: a survey of the geography, government, literature, social life, arts, and history of the Chinese empire and its inhabitants''
*''Account of a Japanese romance''
*''A syllabic dictionary of the Chinese language, arranged according to the Wu-fang yuan yin, with the pronunciation of the characters as heard in Peking, Canton, Amoy and Shanghai''
*''Syllabic Dictionary Of The Chinese Language''
*''A History Of China Being The Historical Chapters From "The Middle Kingdom"''
*''A journal of the Perry expedition to Japan''
*''Narrative Of A Voyage Of The Ship Morrison Captain D. Ingersoll, To Lewchew And Japan, In The Months of July and August, 1837''