Based on the FVCOM hydrodynamic model and the FVCOM-SWAVE wave model, we developed a wave-current coupled storm surge model for the Bohai sea, Yellow sea, and East China Sea during Typhoon “Chan-hom”. Following rigorous validation of surge elevations and significant wave heights, we quantified the impact of wave-current interaction on storm surge and identified key dynamic factors. Findings indicate that wave-current interaction significantly influences surge elevations in near-shore shallow waters, contributing approximately 14% to peak surge water levels. During high tide periods, wave-current interaction tends to reduce surge elevations, but increases surge levels during low tide periods. Accounting for wave-current interaction, the simulated significant wave heights show better agreement with observations. Additionally, the study compares the contributions of tide-surge interaction, wind field, and pressure to surge elevation. The wind field primarily drives surge elevations, with its effects most pronounced in the coastal waters of Zhejiang Province and Hangzhou Bay, where maximum surge elevations reach up to 2 m. In open sea areas, air pressure dominates surge elevations within the typhoon center’s radius. However, in coastal waters, particularly at the head of Hangzhou Bay, nonlinear tide-surge interaction and wave-current interaction significantly impact surge elevations, with respective maxima of 1.2 m and 0.5 m. These findings offer critical insights for enhancing coastal disaster prevention and mitigation strategies.