This study employed a self-developed viscous numerical wave tank based on the piston type wave maker and user-defined functions of Fluent software to explore the wave shadowing effect of the transmission of waves near the underwater object and the reef. In the study, various factors such as the permeability of the reef, changes in topography, and objects motion were considered, and detailed simulation analyses were conducted for five scenarios: a solitary reef, a fixed underwater object, a forced moving underwater object, and a free moving underwater object. The results showed that this method can effectively simulate the complex flow field changes around the underwater object and the reef under different conditions, while also fully considering the strong nonlinearity and fluid viscosity effects between the wave surface and the object. Furthermore, it was found that between the free-moving object and the reef, there would be significant swirls and streamline distortion. This indicates that a portion of the incident wave energy is transformed into kinetic energy of swirls, resulting in a smoother and more uniform flow field and reducing wave forces.