Aiming at the end force/position control problem of flexible manipulator with model uncertainty and external time-varying disturbance, an indirect force/position control method based on generalized proportional integral observer is proposed. Firstly, the dynamic relationship between the final position of the contact surface and the contact force of the manipulator in the workspace is described according to the impedance model, and the parameter uncertainty and external disturbance in the system are regarded as the total disturbance. Then the generalized proportional integral observer is used to estimate and compensate the unknown disturbance, and the sliding mode control technology is used to design the nonsingular fast terminal sliding mode controller, so that the inter relay/position hybrid controller has better stability and robustness in the face of time-varying disturbance without calculating the impedance parameters. The trajectory tracking simulation experiment of flexible manipulator is completed, and the effectiveness of the proposed method is verified.