Coastal evolutions are expected to have a significant impact on storm tides, disproportionately aggravating coastal flooding. In this study, we utilize a nested storm tide model to provide an integrated investigation of storm tide responses to changes in coastline and bathymetry along the Zhejiang coasts. We selected coastline and bathymetry data from 1980 and 2016, as well as data from three typical typhoon events (i.e., Winnie, Haikui, and Chan-hom) for simulating the storm surge processes. The results indicate that changes in the coastline and bathymetry from 1980 to 2016 have resulted in an increase in storm tides in the northern part and a decrease in the central part of Zhejiang. Specifically, storm tides in Hangzhou Bay have increased significantly, with an average increase of about 0.3 m in the maximum storm tides primarily attributed to coastline changes. On the contrary, in smaller basins like Sanmen Bay, while reclamation itself has reduced peak storm surges, rapid siltation has consequently exacerbated the storm surge. By decomposing storm tides into astronomical tides and storm surges, we discovered that the change in tidal levels was twice as significant as the surge change. Moreover, the nonlinear tide–surge interaction was nearly four times that of the pure surge, significantly contributing to storm surge variation. Alterations in the momentum balance reveal that the water depth-induced bottom friction and wind stress increase contributes to the local enlargement of storm tides at the bay head, while the coastline changes exaggerate nearshore storm tides through an increase in the advection term.