To realize the active vibration reduction technology of electric drive gearbox, this paper proposes a multi-objective optimization method of gear modification parameters based on the improved NSGA-II algorithm, a gearbox vibration reduction method based on the optimization of the topology of the gearbox housing and damping materials. The effectiveness of the proposed multi-objective optimization vibration reduction technique is verified by modeling the rigid-flexible coupling dynamics of a dual intermediate shaft type multi-shift electric drive gearbox. The results show that the proposed gear modification parameters can reduce the transmission error peak-to-peak (PPTE) and improve the gear bias load. The proposed housing structure topology optimization method effectively dampens the vibration acceleration of the gearbox.