Taking a spatial parallel robot with flexible joints and links as the research object, a dynamic modeling method for a multi-flexible-body robot system is proposed. Its effectiveness is verified by comparing the numerical model with a simulation model. (1) Background: The elastic deformation of the flexible joints and links in the multi-flexible-body spatial parallel robot under high-speed operation and the coupling effect between the flexible and the rigid components substantially affect the system stability and trajectory accuracy. Therefore, it is necessary to analyze the dynamic characteristics of multi-flexible-body robot systems by establishing accurate dynamic models. (2) Methods: First, the finite element method was used to discretize the flexible joints and links. Subsequently, according to the floating frame of the reference coordinate method, the deformation coordinates of the flexible joints and links were described. The first six modal information were retained to develop a dynamic model considering the coupling effect between the flexible joint and rigid link and between the flexible joint and link. Second, a dynamic model of the end-effector with small displacement changes was established according to the coordination matrix. Furthermore, a dynamic model of rigid links was established based on the vector method and combined with the higher-order dynamic model of flexible joints and links to form the dynamic model of multi-flexible-body kinematic chains. Finally, the dynamic model of the three kinematic chains was assembled with that of the end-effector to obtain an accurate dynamic model of the multi-flexible-body robot systems. (3) Results: The motion trajectory of the multi-flexible-body robot floats around the fully rigid spatial parallel robot in a certain range. Its range of travel in the x, y, and z directions was 0 to 3.14, 0 to 4.06, and 0 to 0.483 mm, respectively. With increasing angular velocity, the maximum absolute amplitude of the driving torque of each branch chain also increases, whereas its motion trend remains unchanged. (4) Conclusions: The proposed dynamic modeling method and its simulation model for multi-flexible-body robots are correct, which can lay a solid foundation for further control performance analysis.