Morton was born in Adams, Jefferson County, New York. He was raised in Detroit and attended the University of Michigan. He was a member of Chi Psi Fraternity at Michigan. After receiving his diploma in 1854, he moved with his bride to Nebraska, which was not yet organized as a territory, and staked a claim in Nebraska City. He was appointed Secretary of Nebraska Territory by President James Buchanan on July 12, 1858 which he served as until 1861.
Respected as an agriculturalist, he sought to instruct people in the modern techniques of farming and forestry. Among his most significant achievements was the founding of Arbor Day. He became well known in Nebraska for his political, agricultural, and literary activities and from there was appointed as Secretary of Agriculture by President Cleveland. He is credited with helping change that department into a coordinated service to farmers, and he supported Cleveland in setting up national forest reservations.
In 1897 Morton planned and began to edit the multivolume Illustrated History of Nebraska. He also published a weekly periodical, The Conservationist. He died on April 27, 1902, in Lake Forest, Illinois, where he was seeking health treatment. His home in Nebraska City is now a state park, the Arbor Lodge State Historical Park and Arboretum.
In 1937, the state of Nebraska donated a bronze statue of Morton to the U.S. Capitol's National Statuary Hall Collection. Morton is a member of the Nebraska Hall of Fame. The J. Sterling Morton Beltway, a highway near Nebraska City, Nebraska, which is made up from U.S. Route 75 and Nebraska Highway 2, is named for him. J. Sterling Morton Magnet Middle School in Omaha, Nebraska also bears his name.
Son Joy Morton was the founder of the Morton Salt Company in Chicago, Illinois, and created The Morton Arboretum in Lisle, Illinois, in 1922. Joy Morton's original Thornhill Estate, began in 1910, has been transformed into a living history museum of over 4,000 different types of trees, shrubs and other woody plants, with the mission to encourage the planting of trees as well as promoting nature as a source of inspiration, wonder and joy, especially for children.