Summary: The dynamic equations of flexible multibody systems with tree topological configuration are derived by using the Jourdain's principle. The independent joint coordinates are introduced to describe the large displacements of the bodies, and the modal coordinates are used to describe small deformations of flexible bodies based on the consistent mass finite element method and normal vibration mode analysis. The minimum differential equations are developed, which are compatible with the equations of multi-rigid body systems or structural dynamics. The stiff problem in the numerical integration is thus alleviated effectively. The method used can be extended to deal with systems with other topological configurations. Finally, the validity and feasibility of the presented mathematical model are demonstrated by a numerical example of a manipulator with two elastic links.