Due to the impact of the elastic deformation of tools and press, and the blank thinning and other factors, the die surface gap is not consistent with the thickness distribution of the stamped part, which leads to low spot rate. With regard to the problem mentioned above, a new mesh mapping algorithm based on binary search was presented, which can realize the accurate mapping between different meshes，and then, a new methodological scheme was developed for the compensation of the die surfaces. In the early design stage, the new methodology can guide the engineer to modify the die surface, thus offsetting the influence on quality caused by the deformation of tools. Application example has shown that the new mapping algorithm not only improves the accuracy but also improves the search speed. The methodology can solve the problem of low spot rate and noticeably improve the first time contacting ratio.