The coaxiality and unbalance are the two important indexes to evaluate the assembly quality of an aeroengine. It often needs to be tested and disassembled repeatedly to meet the double-objective requirements at the same time. Therefore, an intelligent assembly method is urgently needed to directly predict the optimal assembly orientations of the rotors at each stage to meet the double-objective requirements simultaneously. In this study, an assembly optimization method for the multistage rotor of an aeroengine is proposed based on the genetic algorithm. Firstly, a spatial location propagation model is developed to accurately predict the spatial position of each rotor after assembly. The alignment process of the assembly screw holes of the adjacent rotors is considered for the first time. Secondly, a new assembly optimization strategy is proposed to select different assembly data for the specific values of the coaxiality and unbalance, respectively. Finally, a double-objective fitness function is constructed based on the coaxiality and unbalance. The simulation and experimental results show that the assembly optimization method proposed in this study can be utilized to achieve synchronous optimization of the coaxiality and unbalance of an aeroengine during preassembly.