Humphrey was the son of Congregationalist minister and second president of Amherst College Heman Humphrey and his wife Sophia Porter (1785-1868), daughter of Noah Porter [REF].
On April 3, 1847, Humphrey married his second wife, Martha Pope, daughter of Alexander Pope and Martha Fontaine and widow of her cousin, Charles Pope, son of William Pope Jr., and Cynthia Sturgess [REF].