Offshore Zhoushan sediments are a potential area for shallow gas resources in China, where authigenic pyrite is widely distributed. Pyrite content, size distribution, and morphology are influenced by depositional conditions and are sensitive to environmental changes. This study investigated the authigenic pyrites or gypsums of core JC-1 offshore of Zhoushan. Scanning electron microscopy was used to observe the pyrites and identify various aggregations. Changes in lithology, chlorine content, and stable isotope values of organic matter were analyzed to indicate the evolution of ancient marine, floodplain estuary, tidal flat environments, and shallow marine sedimentary facies. The morphology and microcrystalline structure of these types of pyrites can be divided into spherical framboid aggregates, sub-euhedral aggregates, and microcrystalline euhedral pyrites with different sedimentary facies. Gypsum minerals and the coexistence of pyrite and gypsum were found in the enriched authigenic pyrites at the SMTZs. The sources of sulfate formed by authigenic gypsums may originate from overlying seawater and pyrite oxidation, whereas calcium ions may come from the dissolution of carbonate or calcareous shells caused by local environmental acidification. The various aggregations of pyrites observed may be related to SO4-AOM in different environments. The findings suggest that authigenic gypsums form due to local environmental acidification and that the sources of the formed sulfate may be from overlying seawater and pyrite oxidation. This study provides a new perspective for understanding the responses of different sedimentary environments to sea level rise and climate change.