In August, 1861, Morris re-enlisted in the Army as a captain of volunteers. He served on the staff of Brigadier General John J. Peck as Assistant Adjutant General of Peck's brigade during the Peninsula Campaign and from June 24, 1862 to September 1, 1862 as assistant adjutant general of Division 2, IV Corps, Army of the Potomac, after Peck was appointed commander of the division. Morris participated in the Siege of Yorktown, Battle of Williamsburg and Battle of Fair Oaks.