In order to study the coupling dynamic modeling method of a flexible manipulator system with harmonic drive, both the driven model parameters of the harmonic joint and the coupling vibration model of the flexible manipulator are identified. Coulomb friction of the joint is identified using step current excitation and uniform rotation experiments in a low speed. Then, the transfer function model of the harmonic joint is established and identified using a pseudo-random binary sequence excitation, and the moment of inertia and viscous friction coefficient of the harmonic joint are included in this model. Moreover, the predict outputs of the obtained model are in good agreement with the experimental results. The linear relationships between the strain output of the flexible manipulator and the coupling torque are presented from theoretical derivation. The transfer function model from the angular displacement of the servo motor to the strain output of the flexible manipulator are identified. Experimental results show these identified models match well with the proposed structure, both in the time and frequency domains. As a result, this coupling dynamic modeling method of the flexible manipulator system with harmonic drive is accomplished by integrating those two identification transfer function models.