Paleoenvironmental reconstructions of coastal areas during geological history are critical for understanding past responses to marine transgression. Identifying transgressive layers in sedimentary strata is therefore of great importance. To this end, we examined the content and isotopic composition of pyrite sulfur, in combination with classical organic geochemical indicators (e.g., C/N ratio and the δ13C of organic carbon), to trace the marine transgressions along the southeast coast of China since Marine Isotope Stage (MIS) 5. Our results suggest that the mass ratio of total organic carbon and pyrite sulfur (C/S ratio) is sensitive to seawater intrusion. Three transgressive layers were identified by low C/S ratios in core NDGK2, which correspond to sea level rise during MIS5, MIS3, and MIS1. Sediments deposited during MIS1 are represented by low C/S ratios with an average of 2.31, while those deposited during MIS5 and MIS3 have slightly higher C/S ratios, indicating a less extensive influence of seawater. Pyrite production in sediments deposited during MIS5 and MIS3 may have been limited by sulfate supply, as reflected by more positive values of δ34Spyr, whereas pyrites deposited during MIS1 were likely formed without sulfate limitation, as reflected by more negative values of δ34Spyr. The isotopic signals of pyrite sulfur thus further confirm the inference based on the C/S ratio. The magnitude of the transgression increased from MIS5 to MIS1, which is in agreement with the findings from classical organic geochemical indicators examined in this study, as well as geochemical and micropaleontological salinity indicators from previous studies. Our findings provide a promising method for identifying marine transgressions and their magnitude from the depositional record, especially when sedimentary strata lack diagnostic micropaleontological and sedimentological characteristics.