Well, yes, you can watch 3d movie even you have astigmatism. And in my opinion, when you just have a pair of contact lenses which can do a good job for you when you are watching 3d movie. In common, glasses generally rely on dramatically differing lens curvature and thickness which can throw off the distortion effect required for traditional 3D. But on the other hand, contact lenses can balance your eye dominance issues then glasses. And in that way, the thickness and curvature variance negligible to naught and 3D glasses always work fine with contact lenses, even when you have astigmatism. So you can just have a try.
People with astigmatism eyes could also see the 3d movies with the eyeglasses and the 3d glasses. You could also see the movies clearly with good effect. You could also wear the contact lenses with astigmatism role and then wear the 3d glasses to make you look clearly. You could have a try. It will not be bad for your eyes.