Due to the harsh and changeable marine environment, one low speed stator-permanent magnet machine named doubly salient permanent magnet machine with toothed pole is applied for marine current energy conversion system. Indeed, this machine has simple structure, intriguing fault tolerance, and higher power density, which could adequately satisfy the different complicated operation conditions. However, its permanent magnet flux-linkage has the same variation period as the inductance which leads to a strong nonlinear coupling system. Moreover, the torque ripple caused by this special characteristics, uncertainty of system parameters and disturbance of load greatly increases the difficulty of control in this strongly coupling system. Consequently, the classical linear PI controller is difficult to meet the system requirement. In this paper, the high-order sliding mode control strategy based on the super-twisting algorithm for this system is creatively utilized for the first time. The stability of the system within a limited time is also proved with a quadratic Lyapunov function. The relative simulation results demonstrate convincingly that, the high-order sliding mode control has little chattering, high control accuracy and strong robustness.