In this paper, the birefringences of two fluorinated polymers, namely, poly(trifluoroethyl methacrylate) (PMATRIFE) and poly(methacrylate of pentafluorophenyl) (PMAPF), are studied. It is found that the molecular structure and molecular orientation of these polymers are the two main factors influencing the birefringence. The calculations show that the material birefringence (Δn) of PMAPF is greater than that of PMATRIFE by 0.00009, while the intrinsic birefringence (Δn 0) of PMATRIFE is greater than that of PMAPF by 0.0378. The lower Δn 0 of PMAPF is caused by the benzene ring in the repeat unit. On the other hand, the planarity of the benzene ring can enhance the degree of orientation of the PMAPF molecular chains, which is three times larger than that of PMATRIFE, and consequently a larger Δn of PMAPF. Furthermore, the effect of different shear rates on the birefringences of PMATRIFE and PMAPF is examined. The calculations reveal that their Δns are enhanced.