Wave nonlinearity plays a critical role in modulating energy dissipation and sediment transport in vegetated coastal zones, influencing shoreline stability and ecosystem-based defenses. This study analyzes 45 d of wave observations from the Yangtze Estuary, including data collected during Typhoon Khanun, to investigate its spatial variability and underlying mechanisms of wave nonlinearity across a mudflat–vegetation transect. Wave skewness and asymmetry varied within tidal cycles, increasing at low tide and decreasing at high tide. During typhoon conditions, nonlinearity intensified significantly, with skewness increasing by up to 346% and asymmetry shifting toward more forward-leaning waveforms, both closely linked to elevated Ursell numbers. Bispectral analysis at five stations across the transect revealed distinct energy transfer mechanisms: sum interactions dominated over mudflats, whereas difference interactions prevailed within vegetated zones, indicating vegetation-induced modification of nonlinear wave dynamics. Further analysis shows that shoaling and vegetation exerted opposing influences, amplifying and damping wave nonlinearity, respectively. Empirical formulas proposed by Zhao et al. (Coastal Engineering 2024; 192:104543) from laboratory data were evaluated against the field data, demonstrating reasonable performance under extreme conditions. These findings improve mechanistic understanding of wave–vegetation interactions and support the development of nature-based strategies for coastal resilience and sediment management.