Assembly is an essential part of aero-engine manufacturing, and the assembly quality will affect the engine’s stability and service life. Spindle inertia is an essential factor affecting aero-engine dynamic performance. Assembly can affect the spindle inertia of the aircraft engine, which in turn affects the dynamic performance of the engine. This paper proposes a transfer model of spindle inertia based on machining error transmission, studying the variation law of spindle inertia of multi-stage rotors under the influence of assembly, providing an optimized assembly method with minimized spindle inertia. The influence law of machining errors on spindle inertia is analyzed through the simulation and probability density method. The assembly results of the designed rotors verify the effectiveness of the inertia transfer and assembly model. The results show that the spindle inertia of multi-stage rotors is affected by machining errors, and the spindle inertia can be adjusted by changing the assembly methods. This paper provides a new idea for the transmission and adjustment of spindle inertia of assembly rotors.