With consideration of nonlinear factors and external uncertain disturbances existed in an electro-hydraulic position servo system, a nonlinear model based on an electro-hydraulic shaking table is built in order to improve tracking accuracy of a position reference signal. A nonlinear disturbance observer is employed to measure external unknown disturbances and a backstepping controller is designed for the electro-hydraulic position servo system with nonlinear mathematical model. The proposed controller can guarantee the stabilization of the position closed-loop system using Lyapunov theory. Simulation and experiment of the designed controller are made with the external unknown disturbances. Experimental results show that the proposed control strategy is effective to improve the tracking accuracy of the position reference signal of the electro-hydraulic position servo system.