The system is decomposed into input-output subsystem and the zero dynamics subsystem for Flexible Manipulators with uncertain parameters through the output of Manipulators system is redefined. The chatter free fast terminal sliding mode control is proposed to avoid chattering phenomenon for input-output subsystem. It can guarantee the input-output subsystem to converge to zero in finite time. The zero dynamics subsystem is approximation lineared at the equilibrium point to select the design control parameters, and the zero dynamics subsystem is asymptotically stable at equilibrium point. Thus guarantee the entire flexible manipulator system asymptotically stable. The system has strong robustness to the uncertainty of the system. The simulation results are presented to validate the design.