During the assembly of aero-engine rotors, eccentricity and tilt errors along the radial and axial direction result in uneven loading along the mating surface, which significantly impacts the operational lifespan of the rotor. This paper proposes a three-dimensional contour measurement system based on binocular multi-line laser sensing and conducts an aircraft engine rotor stacking virtual assembly technology system, to response the practical requirements of aircraft engine rotor unit production assembly engineering. We combine multi-line structured light active projection device with the binocular stereo vision model to construct the contour measurement system, which enhances the surface features of the projected object by adhering to the common constraint of structured line and stereo vision. Furthermore, the error propagation model for multi-stage rotor assembly to investigate the mechanism of error impact is established aiming to facilitate quantitative research on virtual assembly mechanisms. By manipulating the rotor phases and evaluating the coaxiality under various conditions, effective prediction of phase variation can be achieved, the multi-objective benchmark virtual assembly method based on the error propagation model of multi-stage rotor coaxiality is presented. The experimental results indicate that the proposed measurement system achieves the maximum disparity between the spatial data points procured by the proposed measurement system and the predetermined value of 2.1 μm, and the maximum disparity between the target plane’s average movement distance and the preset value of 3.7 μm. The precision provided by this system effectively meets the objective of assembly phase optimization for multi-stage rotors. In the empirical experiment conducted on the three-stage rotors, both systems yielded identical optimized phases: 0° for the first-stage rotor, 270° for the second-stage rotor, and 120° for the third-stage rotor, thereby validating the efficacy of the proposed measurement and optimization method for aero-engine multi-stage rotors with virtual assembly.