Of course, you can, I am a nearsighted for 8 years. And i have watched 3D movies several times and feel good. Since i am nearsighted, i have very poor vision and always wearing prescription eyeglasses. When i watch 3D movies, i always have to wear two pair of glasses - a pair of 3D glasses over my regular prescription glasses. It's OK.
I am not sure what your vision problem is. If you have glaucoma, you are not suitable to watch 3D movie. Because watching 3D movies in a dark place will make the pupils dilated and intraocular pressure increased. The increased intraocular pressure will damage the optic nerve and then lead to acute glaucoma.