A point set analysis method considering the practical engineering constraints has been proposed in this article. First, the coherent point drift method was used to obtain the initial values of data analysis. Second, the error distribution in different directions was expressed by weight vectors. Last, the multiobjective optimization model was built and the engineering constrains were introduced into the multioptimization objective function to achieve the optimal data analysis results. The experimental results proved that the method could obtain the reasonable data analysis results, which met the engineering constraints. It provides the important basis for the subsequent assembly.