In this paper, a robust neural adaptive controller is proposed for the trajectory tracking control problem of unmanned surface vessels (USVs), considering model uncertainty, time-varying environmental disturbance, and actuator saturation. First, measurement errors in acceleration signals are eliminated through filtering techniques and a series of auxiliary variables, and after linearly parameterizing the USV dynamic model, a parameter adaptive update law is developed based on Lyapunov’s second method to estimate unknown dynamic parameters in the USV dynamics model. This parameter adaptive update law enables online identification of all USV dynamic parameters during trajectory tracking while ensuring convergence of the estimation errors. Second, a radial basis function neural network (RBF-NN) is employed to approximate unmodeled dynamics in the USV system, and on this basis, a robust damping term is designed based on neural damping technology to compensate for environmental disturbances and unmodeled dynamics. Subsequently, a trajectory tracking controller with parameter adaptation law and robust damping term is proposed using Lyapunov theory and adaptive control techniques. In addition, finite-time auxiliary variables are also added to the controller to handle the actuator saturation problem. Signal delay compensators are designed to compensate for input signal delays in the control system, thereby enhancing controller reliability. The proposed controller ensures robustness in trajectory tracking under model uncertainties and time-varying environmental disturbances. Finally, the convergence of each signal of the closed-loop system is proved based on Lyapunov theory. And the effectiveness of the control system is verified by numerical simulation experiments.