The assembly quality of the multistage rotor is an essential factor affecting its vibration level. The existing optimization methods for the assembly angles of the rotors at each stage can ensure the concentricity and unbalance meet the requirements, but it cannot directly ensure its vibration responses meet the indexes. Therefore, in this study, we first derived the excitation formulas of the geometric and mass eccentricities on the multistage rotor and introduced it into the dynamics model of the multistage rotor system. Then, the coordinate transfer model of the geometric and mass eccentricities errors, including assembly angles of the rotors at all stages, was established. Moreover, the mathematical relationship between the assembly angles of the rotors at all stages and the nodal vibration responses was established by combining the error transfer model with the dynamics model of the multistage rotor system. Furthermore, an optimization function was developed, which takes the assembly angles as the optimization variables and the maximum vibration velocity at the bearings as the optimization objective. Finally, a simplified four-stage high-pressure rotor system was assembled according to the optimal assembly angles calculated in the simulations. The experimental results showed that the maximum vibration velocity at the bearings under the optimal assembly was reduced by 69.6% and 45.5% compared with that under the worst assembly and default assembly. The assembly optimization method proposed in this study has a significant effect on the vibration suppression of the multistage rotor of an aero-engine.