In a manor of speaking.
Ganondorf the man can literally turn into Ganondorf the Maou (Demon) but if Ganondorf is destoryed, there's evidance to suggest that Ganon can live on his own.
I think the second time you mentioned Ganondorf you meant to say Ganon.
But doesn't Ganon die? Because in OOT, he was locked away by the sages for 100 years (I think) and then was let free or something. Could that mean that there is only one Ganon?
OoT- Ganondorf is defeated by Link. He turns into Ganon who is also defeated by Link. Ganon/dorf is sealed away (on the AT) in the SR until WW comes.
WW- Ganon/dorf somehow escapes his prison and hundreds of years later a new Link defeats Ganondorf (who seemingly has the spirit of Ganon in his body as well). It is highly debated whether or not Ganondorf is dead at the end of WW or just turned to stone.
OoT CT- Ganondorf is left alone until he does something outrageous that causes him to be captured and sentenced to execution/sent to the Twilight Realm.
TP- Ganondorf uses Zant to escape the Twilight Realm and is defeated by another new Link. Ganondorf turns into Ganon who is defeated by Link. Link stabs Ganon/dorf and it's made pretty clear Ganondorf is dead.
All three of those Ganondorfs mentioned in different games are the same person/demon.
My theory is, that after Ganondorf is killed in TP, FSA introduces a new Ganondorf, but the demon (Ganon) takes over this new Ganondorf's body. Same name, different "human", same demon in his body.
That's my theory anyway. This means 2 things if you follow my theory.
1. There are 2 Ganondorfs, 1 Ganon.
2. The original Ganondorf lives in 2 seperate timelines but that does not mean that they are 2 seperate Ganondorfs. Still the same person, just in parallel timelines.