The invention relates to a secondary polycondensation method of a finite element model of a spacecraft. Finite element physical models of a main structure and all secondary structures of the aircraftare built respectively, then the finite element physical models of part of the secondary structures are subjected to primary polycondensation through a mixed interface mode synthesis method, and the finite element physical models or a primary polycondensation model of the secondary structures and the finite element physical model of the main structure of the aircraft are assembled to obtain a mixed model; finally, the mixed model is subjected to secondary polycondensation to an aircraft-rocket master node of the aircraft and a carrier rocket through a fixed interface mode synthesis method, a rigidity and quality matrix obtained after secondary polycondensation and a transfer matrix corresponding to an internal response point are acquired, and results are output to be used for coupling loadanalysis of the spacecraft and the rocket. The method solves the problem that an existing primary polycondensation method cannot handle secondary polycondensation, calculation and evaluation of polycondensation errors are added, and the calculation efficiency and accuracy are improved.