In order to solve the problem that the residual unbalance mass of dual-rotor aero-engine may cause severe vibration, the modal unbalance influence factor is used to evaluate the sensitivity of the vibration to unbalance, and an optimization design method of residual unbalance mass distribution of dual-rotor system is established. A similar dynamic model of an aero-engine dual-rotor system with inter-shaft bearing and a dual-rotor experimental system based on the similar dynamic model are used to verify the effectiveness of the optimization design method. Theoretical analysis and experimental results show that: the proposed optimization design method of residual unbalance mass distribution of dual-rotor system can significantly reduce the dual-rotor unbalance response under partial modes, and the vibration reduction ratio is not less than 40%. It can effectively improve the overall vibration of dual-rotor system in full working range, and provide some technical reference for the vibration control of aero-engine dual-rotor system.