The interaction mechanisms between waves and marine structures are a popular research topic. This paper applies the weakly compressible smoothed particle hydrodynamics (WCSPH) method to study the dynamics of green water overtopping. To enhance the accuracy of the simulations, the SPH method coupled with the large eddy simulation (LES) model is employed for numerical investigations. Initially, we validate the effectiveness of the model by simulating the generation of solitary waves and irregular waves, as well as numerically reproducing the water surface morphology during the interaction between solitary waves and the deck. Subsequently, the validated model is used to study the dynamic characteristics of different types of waves overtopping, revealing significant variations in their motion. Furthermore, we investigate the effect of deck roughness during the entire green water overtopping process in terms of both protrusions extent and distribution, confirming that a reasonable setting of the protrusions can greatly reduce the wave impact loads on the deck, thereby protecting the structure. Additionally, a three-dimensional model is developed to study the green water problem, and we find that the turbulence phenomenon is more pronounced in the three-dimensional scenario.