Morton was born in East Freetown, Massachusetts to Nathaniel and Mary (Cary) Morton. He received his early education at home, at age fourteen being placed under the Rev. Calvin Chaddock at Rochester, Massachusetts for further instruction. In 1801 he entered Brown University with the sophomore class, came to adopt Jeffersonian ideas, and graduated in 1804. He then read law at Taunton for a year in the office of Judge Seth Padelford, after which he entered Tapping Reeve's law school in Litchfield, Connecticut (where he was a schoolmate of John C. Calhoun). Moving back to Taunton, he was admitted to the Norfolk bar in 1807 and began practising. On December 23 of that year he married Charlotte Hodges, with whom he had twelve children. He received his LL. D. from Brown in 1826, and again (as an honorary degree) from Harvard University in 1840.
After serving as clerk of the Massachusetts Senate, Morton was elected as a Democratic-Republican to the House of Representatives in 1816 and served from 1817 until 1821. He lost his seat in the election of 1820.
In 1823 Morton served on the Massachusetts Governor's Council and became Lieutenant Governor the following year. He served briefly as acting Governor after William Eustis died in office in 1825. Later that year he was named as associate justice of the Massachusetts Supreme Judicial Court, and served there until 1840. As a judge he showed ready knowledge of legal principles, sound judgment in applying them, patience, counrtesy, and strength of character.
From 1824 to 1848 there were two well-defined political camps in Massachusetts. The conservative Whigs were made up of wealthy aristocrats, shipowners, bankers, and manufacturers, largely concentrated in Boston. The more liberal and progressive Democratic-Republicans (who became known as the Democrats in this period) consisted of farmers, workers, and recent immigrants. Morton headed the latter group, and each year from 1828 to 1843 he ran for Governor on its ticket. He defeated Edward Everett in 1839 by a single vote, and the Senate chose him over John Davis in 1842, as neither man obtained a majority. As Governor he secured retrenchment in public expenditures, reduced the number of Supreme Judicial Court justices from five to three, and abolished the right of appeal from the court of common pleas to the SJC except on questions of law, this privilege having made the administration of justice slow, expensive, and uncertain.
In 1845 President Polk appointed Morton collector of the port of Boston; he served four years. In 1848 he refused to run for Vice President with Van Buren, as he could not bring himself to bolt his party. However, his life-long opposition to slavery led him to join the Free Soil Party. He was a delegate of that party to the Massachusetts Constitutional Convention of 1853, and was elected on its ticket to the Massachusetts House of Representatives in 1858, serving one term.
Morton was a man of unquestioned honesty, whose poise, serenity, and character made him generally admired. In his championship of the lower classes, his distrust of over-large corporations, and his advocacy of shorter working hours he was a man ahead of his time (perhaps accounting for his somewhat sporadic level of political success). He was an overseer of Harvard University for thirty-two years.
Morton died at home in Taunton in 1864 and was buried in Mount Pleasant Cemetery there. His home in Taunton later became the original building of Morton Hospital and Medical Center. The Morton House in Taunton was demolished in the 1960s during hospital expansion. The Morton House of East Freetown was moved to Newport, Rhode Island sometime during the 20th century.