Abstract: For a spacecraft with multi-body motion characteristics, such as the multi-axis driven antennas, the manipulator arm’s movement, the transposition of the space station cabin, a flexible multi-body dynamics modeling based on the floating base and the tree topology is used for the computation and simulation combined with the control system. Based on the Lagrange equation and the finite element method, the dynamics equations are derived for the motion of the large-angle rigid body the elastic component vibration, and the flexible joint deformation characteristics. Programs are developed and put to engineering practice for the rigid and flexible coupling dynamics modeling of such kind of spacecraft, so as to ensure the fully autonomous dynamic modeling, the model code output, and the capabilities of the simulation combined with control. The software can be used for the dynamic analysis, the control system design, and the system-level simulation verification. In the actual engineering application, a comparison with the commercial flexible multi-body software Adams is made, to verify the correctness and the versatility of the modeling method and its software implementation.