The present study conducted a comprehensive study on the distribution and source of heavy metals (Cu, Zn, Ni, Pb, Cd) in the sediments of the coastal East China Sea (ECS), one of the most developed regions in China with very active land-sea interactions, using 119 surface sediment samples and a 2-m sediment core collected after super Typhoon Chan-hom in 2015. Heavy metals in the surface sediments exhibited metal-dependent and regional distribution patterns, showing higher levels in the southern inner shelf (SIS) than the Yangtze River estuary (YRE), and generally being evaluated as unpolluted to moderately polluted in the coastal ECS (except few sites adjacent to Xiangshan Harbor were strongly polluted by Cd). Based on the organic carbon isotope compositions (δ¹³C) data as well as the strong correlations between heavy metals and natural major elemental contents (Al₂O₃, Fe₂O₃, and SiO₂), we suggest natural weathering detritus as the major source of heavy metals in the YRE region and the spatial distributions were highly controlled by sediment grain size and organic matter. In contrast, the spatial distributions of heavy metals in the SIS region were less correlated with sediment properties, due to more complex sources and stronger hydrodynamic impacts. The vertical distribution of heavy metals in the sediment core indicated significant enrichments since 1950s, but showed unusual gradually decreasing trends in top layer (30 cm–0.5 cm), attributing to the strong disturbance of super Typhoon Chan-hom on sediment transportation and metal partitioning. Besides, we also observed that heavy metal levels in shallow water regions of Zhejiang coast were reduced due to the passage of typhoon. Such strong impacts of super Typhoon Chan-hom on heavy metal distributions in the ECS indicates that the impacts of extreme hydrodynamic events should raise more concern when assessing the distribution and potential risks of contaminants in coastal regions.