This study is to systematically analyze the influences of time-varying meshing stiffness (TVMS) and meshing impact on the dynamic characteristics of high-speed gear transmission in the two-stage pure electric vehicle (PEV) gearbox, as well as the effect of tooth surface modification on the vibration control. First, the dynamic model was established, and the TVMS and meshing impact were calculated. Then, the vibration characteristics of single-stage and two-stage helical gear transmission were analyzed under three different excitation conditions, excitation of TVMS, excitation of meshing impact, and excitation of both. The results show that the effect of rotating speed on the system vibration is not significant outside the resonant region under the excitation of TVMS, while the effect of meshing impact becomes the main exciting component with the increasing rotating speed. The vibrations of the two gear pairs interact with each other; the vibration frequency of one gear pair contains both its meshing frequency and the coupling frequency of the other gear pair. Tooth surface modification in the input-stage gear pair can reduce the vibration of both the input- and the output-stage obviously; that is, more attention should be paid to the input-stage gear pair in the modification design of PEV gearbox.