This paper proposed configuration three-level matching model based on modular product structure in order to solve the product configuration design problem in mass customization (MC). According to the product structure and the features of configuration design, the model divided the configuration course into three parts as first-level complete matching, second-level similarity matching and third-level correlation matching. Firstly obtained standard module that meets clients’ demands by retrieval algorithm of first-level complete matching and similar module of the customized by mathematical model of second-level similarity matching. Then based on them, analyzed the correlation matrix among modules and associated attributes of modules interface, and established the mathematical model of third-level correlation matching and realized the optimum combination of modules. Finally, verified the model by examples. The results indicate that this model could effectively solve the low-efficiency problem of deformation module recombination design in traditional product configuration so to rapidly respond to clients’ customization demands.