 He was on duty at West Point, 1846–51, as assistant professor of mathematics and assistant instructor in artillery and infantry tactics.He was appointed assistant to the Judge Advocate of the Army at Washington and continued in the discharge of the duties of his position until he resigned his commission in the Army of the United States April 27, 1861.Thus immediately prior to the American Civil War he was on the staff of the Judge Advocate of the Army in Washington, D.C.

With the secession of Virginia in 1861, Jones was commissioned as a major in the State of Virginia corps of artillery on May 1, 1861 in the military force of Virginia and later was promoted to be Colonel.