Traditional variation analysis methods are not applicable to non-rigid assemblies due to possible part deformation during the assembly process. This paper presents the use of finite element methods to simulate assembly deformation. The relationship between the parts variation and the variation of the key points in final assembly for quality control is set up by calculating the spring back deformation after assembly. Moreover, the optimization method for non-rigid assembly variations based on finite element analysis is presented. The optimal objective is to reduce the manufacturing cost. The approach is implemented by using ANSYS and MATLAB. The test example shows that the proposed method is effective and applicable.