As an important manufacturing process, mechanical assembly affects directly product quality. Conventional quality inspections and estimations of mechanical assembly are primarily concentrated in “static quality”, such as size coordination, shaping and positioning tolerances, etc. However, mechanical assembly actually has its own dynamic quality, which contributes to that of whole product. Inspecting only static quality is thus incomplete for quality estimation of the assembly. On the basis of substructuring method, this paper at first applies eigenvalue analysis to investigate the effects of assembling process on the dynamic transfer-functions, expressed by spectral-based frequency response functions (FRFs), of substructural components involved in the process. Eigenvalue modules of FRF-matrix-ratios of FRF before assembling to that after assembling are analyzed to quantify the effects, which are consequently indicated by the mean module. Then, according to the explicit definition of “dynamic quality of mechanical assembly” introduced in this paper, dynamic quality matrix of mechanical assembly and its mean eigenvalue module are worked out and chosen to be the right quantitative measure and indicator for dynamic quality estimation of assembly system. Meanwhile, a lumped-parameter model and its experimental counterpart are employed to validate effectiveness of the analytical outcomes obtained and the quality estimation method established in the study