A high-order nonsingular terminal sliding mode (NTSM) optimal control scheme for an uncertain two-link flexible manipulator system is proposed with considerations of both problems of non-minimum phase and chattering. Through system decomposition into an input-output subsystem and a zero dynamic subsystem by regular form technique, the controllable minimum phase characteristic is achieved, and then a third order NTSM controller is designed to realize fast convergence of the input-output subsystem, as well as to suppress the undesirable chattering. Meanwhile, the stability of zero dynamic subsystem is checked and its control property is optimized by a genetic algorithm around equilibrium points. Simulation results are presented to validate the control scheme.