He married Frances Brewton, (b. June 11, 1733) the sister of Miles Brewton, a wealthy Charleston merchant and slave trader.
During the United States Revolutionary War, Colonel Pinckney fled Charleston with South Carolina Governor John Rutledge, before the surrender of the city to the British. Rutledge intended to carry on a state government in exile in North Carolina. Colonel Pinckney however returned to Charleston and swore loyalty to British authority, who allowed him to keep his property. This was unpopular among the revolutionary forces, and in February 1782, the South Carolina legislature voted a 12% amercement of Colonel Pinckney's property to punish his switch of allegiance.
On his death in 1782, he left the Snee Farm and other property to Charles, his oldest surviving son.