Abstract: In order to overcome the difficulties of transmission calculation of arbitrary polarized electrical-magnetic waves passing through anisotropic materials by means of the traditional transfer matrix,1-D photonic crystal with magnetic defect was designed.After incident elliptically polarization wave is decomposed into left-handed and right-handed circular polarized waves,a transfer matrix for dealing with anisotropic material and arbitrary elliptically polarization was deduced.The result indicates that the change of polarization states of reflected and transmitted waves from 1-D photonic crystal can be determined by means of this new method.