This paper addresses challenges in unmanned surface vessel (USV) trajectory tracking, such as significant errors induced by wind and waves, limited adaptability of adaptive gains, and vibrations in sliding mode control. A novel adaptive Super-Twisting sliding mode control algorithm is proposed to mitigate these issues. The USV mathematical model, derived from its structure, is transformed into a second-order system differential equation using trajectory reference points. An adaptive Super-Twisting sliding mode controller is designed, and adaptive gains ensuring closed-loop system stability are derived through the construction of a Lyapunov function. Simulation experiments, considering wind and wave resistance, compare the proposed method with Super-Twisting sliding mode control and traditional adaptive Super-Twisting sliding mode control. Results demonstrate a reduction in average tracking errors of 0.60 m and 0.27 m, respectively, over a 30-second simulation period, affirming the effectiveness of the proposed method in enhancing system control performance, suppressing vibrations, and reducing trajectory tracking errors.