In this paper, an observer-based sliding mode controller is proposed for a high-accuracy motion plant to suppress the disturbances and improve the tracking performance. In particular, a two time-scale separation technology, which can recover the disturbance state in a faster time scale, is utilized to compensate the disturbances and improve the system robustness. The parameter identification is carried out to obtain the model coefficients with a high fitting rate. Such an identified model can allow the engineers to tune the controller’s gains highly enough when the system suffers from the measurement noises. Instead of the traditional low-pass filter, a differentiator is introduced for the velocity signal prediction and its discrete-time version is provided to attenuate the noises effect. To verify the effectiveness of the proposed approach, an adaptive robust control law is compared with the proposed one in terms of dynamic positioning error, robustness and rapid signal tracking, and the superiority and advantages can be illustrated by the experimental results.