According to the symmetry of transmission matrix for non-uniform magneto-optic fiber Bragg gratings (MFBGs), the simulation model of the non-uniform MFBGs with bidirectional injection of light has been presented for the Optisystem software. The simulation model is verified by comparing with the Matlab numeric results using the piecewise-uniform MFBG model. As an example, the polarization-dependent loss (PDL) of an MFBG-based Sagnac interferometer (MSI) is analyzed in detail. Simulation results indicate that the magnetic field sensitivity of the MSI system can be improved by optimizing the coupling coefficient of the coupler, and the maximum of peak PDL is up to three times that of the single MFBG structure. The simulation model proposed in the paper is useful for the design of MFBG-based optical information devices.