The manufacturing/assembly error of machine parts is a key factor that influences the performance and economy of mechanical systems. To achieve high assembly precision and performance on the basis of low manufacturing accuracy and cost, this study primarily optimizes the assembly error of machine parts. First, the small displacement torsor is used to characterize the small deformation between the mating surfaces of parts. Subsequently, to realize the combination of small displacement torsor and tolerance, the small displacement torsor with manufacturing error and assembly deformation is mapped to the tolerance domain. Second, based on the relationship between small displacement torsor and tolerance, an assembly error optimization model is established on the basis of the conventional tolerance-cost model, considering the emergence of manufacturing error and assembly deformation. Third, aiming at the high-pressure rotor for aeroengines, the error optimization design of assembly is carried out developed with the assembly accuracy requirement as the constraint condition, and the total costs of the manufacturing and assembly processes as the objective. The optimization results indicate that the manufacturing error range of each mating surface after optimization changes, from small to large, under the premise of ensuring the product’s performance, which verifies that the difficulty in processing parts is reduced, and that the efficiency of parts processing is also improved. Meanwhile, the relative manufacturing cost after optimization is reduced by 6.79%, which reflects the economic requirements to a certain extent. The content of this article provides the necessary design basis and reference for the realization of high assembly accuracy of mechanical systems, under low cost requirements from the design perspective.