The purpose of this paper is to provide empirical evidence for the validity of the relationship between service-oriented manufacturing information system (SMIS) customization and performance from three aspects: data flexibility, process flexibility and system flexibility. We select some questionnaires from the third round of High-performance manufacturing (HPM) data to construct the construct, verify the reliability and validity of the construct, extract principal components, and analyze the mediating effect by using multiple chain linear regression and structural equation model. The results show that SMIS customization has a significant impact on its performance, and this effect works through its flexibility. More specifically, it is the multiple chain mediation effect composed of data flexibility, process flexibility and system flexibility. The importance of SMIS customization and flexibility to the organization is made clear, which helps practitioners understand the internal mechanism that affects SMIS performance, so as to use limited resources to improve system performance.