He volunteered for the American Civil War and joined the Union Army, being commissioned as Captain in the 1st Ohio Infantry Regiment. He took part in the battles of Shiloh and Stones River, in the later as ordnance officer on the staff of the XX Corps under Maj.Gen. Alexander M. McCook, his former regimental commander. Afterwards he became and aide and adjutant to Maj.Gen. William S. Rosecrans when he commanded the Army of the Cumberland, though eventually returning to the XX Corps as its Chief of Staff. Thruston fought in the Battle of Chickamauga and continued his staff work under Maj.Gen. George H. Thomas during the Atlanta Campaign. He eventually was promoted up to Lieutenant Colonel and served as Judge-Advocate General of the Army of the Cumberland; afterwards being brevetted Brigadier General for his services during the war. Toward the end of the Civil War and during early Reconstruction, Thruston established provost courts, arguing that the only means for African-Americans to be accorded equal treatment under the law was through the supervision of the Army.