We demonstrate the combined effects of SPM, GVD, and PMD-induced eye-diagram penalties by means of numerical simulations for 40Gbit/s NRZ and RZ modulation formats. Considering all orders of PMD, we choose a fixed state of input polarization (SOIP) and do the simulation 1000 times for each input average power, and then get the Q-penalty of eye-diagram by exponential extrapolation method for cumulative probability 10-5. When input average power is less than 0dBm, SPM effect is very weak and GVD is compensated completely, only PMD takes effect in this power area. The Q-penalties are constants for NRZ and RZ with different PMD values. As input average power increasing, SPM takes effect gradually. First order PMID can suspend the SPM affection, and the higher PMD value, the more postponement is observed. The Q-penalty contributed by higher order PMID has close relation with spectrum width of signal. For NRZ signal with chirp=-0.7, the interactions between SPM and chirp can decrease spectrum width of signal; the Q-penalty contributed by higher order PMD will decrease correspondingly. For RZ with duty 0.3, the changing of the root mean square (RMS) spectrum width induced by the interactions of SPM and chirp is not obviously in this case, the Q-penalties of SPM+GVD+PMD increase consistently. When SPM effect is too strong (For example: for NRZ, average power larger than 10dBm; for RZ with duty 0.3, average power larger than 6dBm.), the interactions of SPM+GVD+PMD will cause the seriously degradation of system performance for any duty cycle and PMID value. Under our simulation conditions, the narrower pulse-width, the less Q-penalty until duty cycle decreases to 0. 1.