This paper presents a dynamic model of a planar flexible inverted pendulum system under the frame of multi-body dynamics by floating frame of reference formulation(FFRF).By proper simplification and linearization,the state space equation of the system was established for linear analysis and control design.The simulation method for such a coupled system by multi-body dynamics program was also provided.The designed controller with a simple low-pass filter for the flexible inverted pendulum was validated by the simulation of a simple flexible pendulum sample.The result demonstrates a new method of designing and verifying a feedback controller of a flexible multi-body system.