Morton was born in Adams, Jefferson County, New York. He was raised in Detroit and graduated from 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, Caroline Joy French, to Nebraska, which was not yet organized as a territory, and staked a claim in Nebraska City. Soon after arriving at Nebraska City, Morton became the editor of the local newspaper, the Nebraska City News. Morton served in the Nebraska Territorial House of Representatives in 1855-1856. He was then appointed Secretary of Nebraska Territory by President James Buchanan on July 12, 1858, which he served as until 1861. He also served as Acting Governor from December 5, 1858, to May 2, 1859.
Respected as an agriculturalist, Morton sought to instruct people in the modern techniques of farming and forestry. Among his most significant achievements was the founding of Arbor Day(from the Latin arbor, meaning tree) is a holiday in which individuals and groups are encouraged to plant and care for trees. It originated in Nebraska City, Neb., in the United States in 1872. J. Sterling Morton is the founder of Arbor Day. The first Arbor Day was held on April 10, 1872, and an estimated 1 million trees were planted that 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 Conservative. He died on April 27, 1902, in Lake Forest, Illinois, where he was seeking health treatment. Morton's wife Caroline died in June of 1881. The Morton 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 National Statuary Hall Collection at the United States Capitol. 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.
His 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 400-acre (1.6 km2) Thornhill Estate, began in 1910, has been transformed into a 1,700-acre (6.9 km2) 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.
Though Morton was a "Bourbon" (i.e. conservative) Democrat, his son, Paul Morton, served as Secretary of the Navy under President Theodore Roosevelt from 1904 to 1905 as a Progressive Republican. It is worth noting that this shift is paralleled by that of Henry Cantwell Wallace, who served as a Progressive Republican Secretary of Agriculture under Harding and Coolidge, and his son Henry A. Wallace who served in the same office as a Democrat under Roosevelt.