I don't know how you ride so this is just an assumption but do you put alot of pressure on her mouth? This can include just in general or pressure to try to keep her head still. If so, she might not like that. Alot of horses don't like it when the reins are short. In that case, whenever you feel her throwing her head, just give her rein and make her push against herself so she's only making herself uncomfortable.
It might also just be a habit or a thing that she's always done. If so, try looking into check reins or a strong martingale. Both prevent the horse from putting his/her head up super high. The check reins also prevent the horse putting his/her head down all the way.
If you have a trainer I definately recommend you ask him or her about it or a vet if you think its a health or body related problem.
Hope this helped!