Autonomous navigation is critical to the development of next-generation shipping systems. The proposal of intelligent ships enables innovation in the shipping and shipbuilding industry and increases the safety and efficiency of ship operations. Autonomous control of surface ships to follow a prescribed trajectory is critical in a variety of maritime applications. This paper proposes a trajectory tracking control strategy for autonomous surface ships that combines nonparametric modelling using Gaussian Process Regression (GPR) with the Model Predictive Control (MPC) framework. A Bézier curve-based Virtual Ship(BVS) guidance strategy is proposed to convert dynamic trajectory points into reference heading angles and speeds, such that the trajectory tracking problem can be decomposed into heading control and speed control problems. Gaussian process regression is utilised to identify the correlation between propeller revolution speed and ship speed, as well as the correlation between rudder angle and heading angle based on experimental data. Two GPR models are therefore constructed as the prediction models for designing MPC controllers for heading control and speed control, respectively. Nonlinear optimisation algorithms are utilised to search for optimal control commands in each sampling interval to solve the optimisation problem in MPC with GPR models and input constraints. Simulations are carried out to evaluate the effectiveness of the proposed method.