In this paper, we developed a high-fidelity model to handle large overall motion of multi-flexible bodies. As a demonstration, the model is applied to a planar flexible beam system. An explicit expression of the kinetic energy is derived for the planar beams. The elastic strain energy is described via an accurate beam finite element formulation. The Hamilton equations are integrated by a symplectic integration scheme for enhanced accuracy and guaranteed numerical stability. The Hamilton and the corresponding Hamilton’s equations of beam vibration problems are formulated. It appears that the proposed symplectic finite elements are capable of providing accurate and robust simulation in the dynamic modeling of multi-flexible bodies systems with large overall motions.