Many industries, such as human-centric product manufacturing, are calling for mass customization with personalized products. One key enabler of mass customization is 3D printing, which makes flexible design and manufacturing possible. However, the personalized designs bring challenges for the shape matching and analysis, owing to the high complexity and shape variations. Traditional shape matching methods are limited to spatial alignment and finding a transformation matrix for two shapes, which cannot determine a vertex-to-vertex or feature-to-feature correlation between the two shapes. Hence, such a method cannot measure the deformation of the shape and interested features directly. To measure the deformations widely seen in the mass customization paradigm and address the issues of alignment methods in shape matching, we identify the geometry matching of deformed shapes as a correspondence problem. The problem is challenging due to the huge solution space and nonlinear complexity, which is difficult for conventional optimization methods to solve. According to the observation that the well-established massive databases provide the correspondence results of the treated teeth models, a learning-based method is proposed for the shape correspondence problem. Specifically, a state-of-the-art geometric deep learning method is used to learn the correspondence of a set of collected deformed shapes. Through learning the deformations of the models, the underlying variations of the shapes are extracted and used for finding the vertex-to-vertex mapping among these shapes. We demonstrate the application of the proposed approach in the orthodontics industry, and the experimental results show that the proposed method can predict correspondence fast and accurate, also robust to extreme cases. Furthermore, the proposed method is favorably suitable for deformed shape analysis in mass customization enabled by 3D printing.