I want to start a new game with NOD but will I loose my game with GDI if I do?

Each time you start a new game, you start as either GDI or Nod on the selected world. You start from the beginning and research units, begin at level 1, etc. You can return-to/start-playing another world by selecting the change world link in the Tiberium Alliances Home Page.

To play both GDI and NOD you need two accounts. The progress on each account is separate so you'll not lose the progress on GDI if you switch. It's best to start both at similar times or the progress on one will seem slow as each one starts at level 1, from the beginning of launching onto the world.

Ok, so I can start playing another world as NOD and then switch back and forth between them

So I need two seperate account, that's what I was thinking was thinking

Yes, 2 separate accounts - one NOD and one GDI (you could have more, but keeping them going is expensive in time and cash.)