Born in Great Barrington, Massachusetts, Lynes was the younger son of Adelaide (Sparkman) and Joseph Russell Lynes. His older brother was the photographer George Platt Lynes.
He graduated from Yale in 1932 and two years later married Mildred Akin, who was a Vassar graduate, the step-daughter of artist Henry Ives Cobb, Jr. and a granddaughter of George W. Wickersham, U.S. Attorney General under William Howard Taft. Lynes started as a clerk at Harper & Brothers, the publishing house, from 1932 to 1936 and was director of publications at Vassar in 1936 and 1937. He then took a job at the Shipley School in Bryn Mawr, Pennsylvania, where he was assistant principal from 1937 to 1940, then principal until 1944. He then joined Harper's Magazine as an assistant editor and became managing editor in 1947, a position he would hold for the next twenty years.