Your question is a little ambiguous. Congress establishes the training regime of the various state national guard units. The regular military (Army, Air Force) has liason offices in charge of coordination with the national guard. However, the appointment of officers, etc. is, I believe still under the control of the states and the state government controls the guard unless it is called into the federal service.
The performance of National Guard officers was so abysmal and the unit readiness was so low at the outset of WWII that a big push was made to give the regular military a lot more control. However, the guard had and has lots of political clout and I don’t think it came to anything.
As tomndebb says, though, it has become a lot easier for the president to federalize guard units as time goes by.