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In this paper, we simulate the effect of Polarization Mode Dispersion(PMD) on 40 Gb/s dispersion compensation transmission system by resolving the coupled nonlinear Schrodinger equation, and calculate the performance of system with different duty cycle order and chirp of the super Gaussian pulse. The results show that the performance of the system changes with these parameters, and there is a group of optimum parameters for the optimum performance of the system.