The effects of tooth modification on the nonlinear dynamic behaviors are studied in this paper. Firstly, the static transmission error under load combined with misalignment error and modification are deduced. These effects can be introduced directly in the meshing stiffness and static transmission error models. Then the effect of two different type of tooth modification combined with misalignment error on the dynamic responses are investigated by using numerical simulation method. The numerical results show that the misalignment error has a significant effect on the static transmission error. The tooth crowning modification is generally preferred for absorbing the misalignment error by comparing with the tip and root relief. The tip and root relief can not resolve the vibration problem induced by misalignment error but the crowning modification can reduce the vibration significantly.