"The President, as Commander-in-Chief, is ultimately responsible for ensuring that the law is enforced and when appropriate, that mercy is granted," White House Press Secretary Stephanie Grisham said in a statement.
Army Green Beret Maj. Mathew Golsteyn was accused of killing an Afghan man in 2010. He claimed he killed the man, an alleged Taliban bombmaker, in an ambush.
Former Army 1st Lt. Clint Lorance, who is serving a 19-year murder sentence at Leavenworth federal penitentiary in northeast Kansas, was convicted of ordering an enlisted soldier to open fire on a group of unarmed Afghans in 2012.
An NBC News report said at the court-martial, several of Lorance's soldiers testified the Afghan men posed no imminent threat.
In the third case, Trump restored Navy SEAL Edward Gallagher to the rank of chief petty officer. Gallagher was convicted by a military jury in July of posing with a dead IS fighter but acquitted on six other counts, including war crimes.
Some U.S. commanders have raised concerns that Trump's move will undermine the military justice system, said a Washington Post report.
"Pardoning war crimes dishonors the military," two scholars, Andrew Bell at Indiana University-Bloomington and Thomas Gift at University College London, wrote in their article carried by the news daily TheHill website.