Ship wakes significantly impact waterway safety and ecological environments, attracting ongoing research attention. Traditional simulations typically address only open waters with regular depth changes, neglecting complex scenarios involving wind-generated waves, irregular topography, or vegetation. This study develops a new simulation method based on wave spectrum equations for complex environments. The approach involves algorithms for water depth identification, vessel positioning, and heading recognition, establishing a boundary generation program for various conditions. By integrating with established models like SWAN and MIKE SW, the method simulates ship wake propagation across complex terrains. Using the Zongyang Xiaogang Channel as a case study, the research analyzes wave processes near hydraulic structures under different navigation scenarios, considering submerged topography, vegetation effects, and wind-generated waves, demonstrating the method’s feasibility for practical applications.