The interaction between waves and offshore structures is one of the central issues in marine engineering. Traditional physical model tests are limited by cost and scale effects; therefore, the development of high-precision numerical methods is crucial for elucidating the mechanisms of fluid-structure interaction. In this study, a three-dimensional numerical wave tank was constructed based on the moving particle semi-implicit (MPS) method, combined with graphics processing unit (GPU) parallel acceleration technology, enabling high-fidelity simulation of nonlinear regular waves. Through tests of damping and wave-attenuation layer parameters, the optimal damping coefficient was determined, effectively suppressing end reflections. Numerical results indicate that the tank can stably generate preset waves with good convergence; for dimensionless wave numbers less than 2, the deviation of the average wave height from the theoretical value is less than 4%, though model performance declines beyond this range. Further simulations of the floating structure's motion response showed that the time-history curves of the caisson's motion agreed well with experimental data, verifying the model's feasibility for wave-structure interaction problems. This study provides a reliable numerical method and theoretical reference for predicting the motion of floating structures under complex wave conditions.