In this paper, a backstepping finite time sliding mode control algorithm considering the system total disturbance is designed for the trajectory tracking control of multi-joint manipulator with model parametric perturbation and external bounded disturbances. Firstly, the system dynamics model is formulated as a strict feedback form, and the uncertainty factors such as model parameter perturbation and external bounded disturbances are considered as the total disturbance of the system which is then estimated by a nonlinear extended state observer developed for improving the robust performance of the system. Secondly, the backstepping finite time sliding mode controller is designed based on the traditional backstepping method and the finite time sliding mode control technique. Finally, the Lyapunov stability theory is employed to prove that the position vector of the multi-joint manipulator can stably track the desired position vector within finite time. The comparison of simulation results is presented to verify the effectiveness of the proposed method.