Jones was appointed a midshipman in the United States Navy in 1836, and served extensively at sea, receiving promotion to the rank of lieutenant in 1849.

During the 1850s, Jones was involved in development work on navy weapons and served as ordnance officer on the new steam frigate Merrimack when she began active service in 1856.

Later in 1862, he commanded a shore battery at Drewry's Bluff, on the James River, and the gunboat Chattahoochee while she was under construction at Saffold, Georgia.

For his "gallant and meritorious conduct" during the battles of Hampton Roads and Drewry's Bluff, Jones was promoted to the rank of commander on April 29, 1863.

For the rest of the Civil War, he supervised the manufacture of badly needed heavy guns for the Confederate armed forces.