As the division over slavery grew between northern and southern states, Morton became active in the development of the Confederacy.

On November 30, 1860, he was chosen to represent Santa Rosa County as a delegate of the Florida Secession Convention in Tallahassee.

On January 7, 1861, he was appointed to be part of a twelve-person committee to prepare an Ordinance of Secession for Florida.

On January 17, 1861, Morton was appointed to be a delegate to the Montgomery Convention for constructing a provisional Confederate government.

Jackson Morton returned to Santa Rosa County and died at his home, "Mortonia", on November 22, 1874.