This paper presents the position tracking performance of the robot system with uncertainties and external disturbances by using super twisting sliding mode control (STSMC) with fractional order (FO) sliding surface. In this scheme, fractional calculus theory is applied to the design of the sliding surface of STSMC, which can reduce the chattering caused by the switch control action and ensure that the control system has strong robust characteristics and fast convergence. Based on Lyapunov stability theory, the controller ensures the existence of sliding mode of sliding surface in finite time. Moreover, an adaptive STSMC reaching law is adopted. By using the fractional order nonlinear switching manifold and adaptive reaching law, the control performance can be obtained more effectively in sliding mode phase and the reaching phase, respectively. Finally, in order to validate the effectiveness and robustness of the proposed control strategy, the linear PID control strategy and the classical STSMC strategy are designed for comparative analysis, and the numerical calculation is carried out according to the dynamic model to study the position tracking accuracy of the robot under uncertainty and external interference.