He was the son of Joseph John Clinch, Jr. (1754–1795), an American Revolution veteran of both the Continental Army and the North Carolina Militia (Edgecombe County Regiment) who attained the rank of colonel.

Joseph Clinch also served in political office, including justice of the peace and member of the North Carolina House of Commons.

In 1816, he commanded forces in southern Georgia, and was ordered by General Andrew Jackson to attack Seminole positions at Negro Fort, an abandoned British post along the Apalachicola River which had become a safe haven for escaped slaves.

Supported by gunboats, Clinch's attack on the outpost caused a major incident when an explosion, resulting from naval artillery hitting the fort's powder magazine, resulted in the deaths of hundreds of Seminoles and slaves, contributing to the beginning of the First Seminole War.

In response, Clinch ordered Major Francis L. Dade to leave Key West and bring his company of men to Fort Brooke.

I had been taught when living at St. Augustine to regard General Clinch as a strict unfeeling disciplinarian but I learned how good men are often maligned.

Picture the image of an old gray-haired man of 5 ft. 10 inches, of muscular build, weighing over 250 pounds, sitting upon the dirt floor, giving counsel and comfort to a poor dying private soldier.

His food was plain and many times I saw him dining with his staff on pork and beans, occasionally getting a beef day like the rest of us.

[5] In the Civil War, the 5th Georgia Volunteer Infantry's first company was also named after him, as the regiment originated from Clinch County.

[10] His son, Colonel Duncan Lamont Clinch Jr., commanded the 4th Georgia Cavalry CSA during the American Civil War.