The response of typical environmental factors in Zhoushan Fishery, including sea surface temperature (SST), sea surface salinity (SSS), and chlorophyll a (Chl-a), before and after Typhoon In-fa was analyzed using satellite data and reanalysis data in this study. Additionally, this study simultaneously elucidated the mechanism by which the typhoon affected these factors. The results showed that: (1) the strong vertical mixing caused by In-fa provoked a decrease in SST, while the asymmetric typhoon wind stress and vertical difference in temperature structure before the typhoon caused a more robust cooling of SST on the right side of the In-fa track; (2) despite the strong mixing and inflow of hypersaline seawater increasing SSS, the combined effect of intense rainfall and diluted water inflow caused an overall decrease in SSS after In-fa’s landing; (3) In-fa caused the Chl-a concentration to decrease first and then increase. The high cloudiness and low Chl-a seawater inflow inhibited the phytoplankton growth during the typhoon, while the abundant light, rich surface nutrients under the upwelling effect, and transport of rich land-based substances induced rapid phytoplankton reproduction after the typhoon; and (4) the change in Chl-a concentration, current, temperature, and salinity induced by a typhoon are essential factors that affect fish behavior and community composition in fisheries. This study provides a point of reference to reveal the response of environmental factors to typhoons and their effects on fishery resources in fisheries located on nearshore estuarine shallow waters with intensive islands.