The Marines said on Wednesday that 2nd Lieutenant Nathan Phan, the officer, was charged with three counts of assault and one count of making a false official statement relating to the incident on April 10, near Hamdania, a town west of Baghdad.
Phan, 26, was the platoon leader of the troops charged with premeditated murder in the fatal shooting of an Iraqi man on April 26 in the same town, the Marines said; but he was not charged in relation to that incident.
Prosecutors accused Phan of putting an unloaded M9 pistol into the mouth of one of the civilians and choking him. They said Phan struck another civilian with closed fists and knees in the face, head and torso, and choked a third civilian.
The military said Phan in all three cases used "force likely to produce death or grievous bodily harm."
Seven Marines and a Navy medic were charged in June with premeditated murder in the man's killing. All could face the death penalty if convicted.
There have been a number of cases involving misconduct by US troops in Iraq, although US military leaders maintain the vast majority of American troops have conducted themselves honourably. Very few of those charged have been officers.