Marine current energy is attracting more and more attention in the world as a reliable and highly predictable energy resource. However, conventional proportional integral (PI) control will be sensitive to the numerous challenges that exist in a marine current turbine system (MCTs) such as marine current disturbance, torque disturbance and other uncertain parameters. This paper proposes a fuzzy adaptive backstepping control (F-A-BC) approach for a marine current turbine system. The proposed F-A-BC strategy consisted of two parts. First, an adaptive backstepping control approach with the compensation of disturbance and uncertainty was designed to improve anti-interference of the MCT so that the maximum power point tracking (MPPT) was realized. Then, a fuzzy logic control approach was combined to adjust parameters of an adaptive backstepping control approach in real time. The effectiveness of the proposed controller was verified by the simulation of a direct-drive marine current turbine system. The simulation results showed that the F-A-BC has better anti-interference ability and faster convergence compared to the adaptive backstepping control, sliding mode control and fuzzy PI control strategies under disturbances. The error percentage of rotor speed could be reduced by 3.5% under swell effect compared to the conventional controller. Moreover, the robustness of the F-A-BC method under uncertainties was tested and analyzed. The simulation results also indicated that the proposed approach could slightly improve the power extraction capability of the MCTs under variable marine current speed.