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This paper studies the transient and steady performance constraints on flexible joint manipulator system with exogenous disturbance, and proposes a fixed-time prescribe performance tracking control method based on the singular perturbation model. For the fast subsystem, a subcontroller with superior transient performance is proposed that guarantees the suppression of flexible vibration in fixed-time. The remaining slow subsystem can be linked with rigid methods to achieve output constraints, a type of time-varying error constraint boundary is first constructed, which broadens the initial error constraint boundary of the time-varying tangent barrier Lyapunov function. Then, a slow subcontroller based on a non-singular fast-integration terminal sliding mode is constructed to make any initial tracking error converge in fixed-time. Finally, a nonlinear disturbance observer is used to counteract the exogenous disturbance. The simulation results show that the controller achieves the prescribe performance.