Thomas Morgan, JP (7 September 1664 – 16 December 1700) was a Welsh Whig politician of the 17th century.
The eldest son of William Morgan and his first wife Blanche, Morgan inherited his father's estate upon the latter's death in 1680. He married Martha Mansel, by whom he had several children, all of whom predeceased him.
Morgan entered the House of Commons in 1689 as Member of Parliament for Brecon, and was High Sheriff of Monmouthshire the same year. In 1690, he sat as MP for Monmouthshire instead, and continued to be returned there for the rest of his life. He also unseated Jeffrey Jeffreys at Brecon in 1698, who appealed on petition. Before the matter could be resolved, Morgan died of smallpox in 1700. His estates, valued at £7000, went to his brother John Morgan.