By signing Executive Order 9981 how did Truman change the U.S. military after World War II?

It would no longer be segregated. Black and White Americans would fight together in the same units.

Ad Hoc desegregation during World War 2 helped this along considerably. It had been thought that mixing of the races would lead to conflict that would lessen combat efficiency. In actual cases the help was appreciated. This was based on after action polling of the troops and officers involved.

In World War 1 the segregated unit 369th Regiment (Harlem Hell Fighters) was given to the French who had many Colonial (Black) units from North and West Africa. The unit fought well.

The Canadian Army was partially segregated during World War 1 as some recruiters were prejudiced against blacks enlisting. There were however many blacks allowed to enlist. An all black construction battalion was raised. There was no segregated units in the Canadian Army during World War 2 but there was still some issues with recruiters.