Chairman of the Joint Chiefs of Staff, Air Force General CQ Brown - America's highest-ranking general and only the second black general to serve as chairman - was fired with immediate effect.
The president will also replace the head of the US Navy, a position held by Admiral Lisa Franchetti, the first woman to lead a military service, and the Air Force vice chief of staff, the Pentagon said.
On Friday, Mr Trump said: "I want to thank General Charles 'CQ' Brown for his over 40 years of service to our country, including as our current Chairman of the Joint Chiefs of Staff.
Senator Jack Reed of Rhode Island, the top Democrat on the Senate Armed Services Committee said: "Firing uniformed leaders as a type of political loyalty test, or for reasons relating to diversity and gender that have nothing to do with performance, erodes the trust and professionalism that our servicemembers require to achieve their missions.".
He is also removing the judge advocates general for the Army, Navy and Air Force, critical positions that ensure enforcement of military justice.
