Jefferson was the son of Nathaniel Jackson of Jay, Franklin County, Maine and Nancy Goodwin(Godwin) Jackson of Rumford, Oxford County, Maine. Nathaniel was married twice. Nancy and Nathaniel were married on 01 August 1814 in Jay, Franklin County, Maine. Nancy and Nathaniel had two children. They were: Huldah Fuller Jackson was born on 29 November 1815; and Jefferson J. Jackson was born on 26 September 1817. Both children were born in Jay, Franklin County, Maine.

Jefferson was married three times. Jefferson married Louisa(Louise) W. Bailey about 1840. Louise and Jefferson had twelve children. They were: Aurintha A. Jackson was born on 09 December 1841 in Hamlin Gore Plantation, Oxford County, Maine; Andrew Jackson was born on 04 September 1843 in Hamlin Gore Plantation, Oxford County, Maine; Sarah Eliza Jackson was born in 1847 in Hamlin Gore Plantation, Oxford County, Maine; John W. Jackson was born on 20 October 1849 in Hamlin Gore Plantation, Oxford County, Maine; Jefferson J. Jackson was born on September 1853; George E. Jackson was born on 13 December 1854; Huldah C. Jackson was born in 1856; Clarence E. Jackson was born in 1858; Joseph A. Jackson was born in 1862 in Milton, Oxford County, Maine; Auburn Jackson was born on 05 August 1863 in Milton, Oxford County, Maine; George L. Jackson was born in 1866 in Milton, Oxford County, Maine; and Sarah Jackson was born in 1874 in Milton, Oxford County, Maine. Jefferson married Adlaide Swan in 1874 in Milton, Oxford County, Maine. Adlaide and Jefferson had three children. They were: Vern Jackson was born about 1874; Huldah Louise Jackson was born in January 1875; and Cuvier Albert Jackson was born in 1878. All the children were born in Milton, Oxford County, Maine. Jefferson married Drusilla F. Putnam in 1878 in South Rumford, Oxford County, Maine. Drusilla and Jefferson had no children.