The pose of spacecraft can be adjusted automatically, intellectualized, high-precisioned by 6 DOF parallel spacecraft assembly platform, resolved the problem of high-precision spacecraft assembly. In digital assembly process, spacecraft assembly platform is used as the positioning mechanism for spacecraft, but it occurs structure deformation caused by spacecraft, which can affect the precision of assembly. This work focuses on the research about the deformation error and proposes a corresponding error compensation method in order to satisfy high-precision requirement in the procession of assembly. To take account of deformation of all parts in the assembly platform, finite element method is applied. Firstly, this paper verifies the feasibility of deformation analysis based on finite element comparing with the stiffness matrix method. Secondly, it establishes a posture error model for the platform. Finally, it proposes an error compensation method based on finite element analysis results and tests the compensation method.