The mud deposit areas on continental shelf have developed in a relatively steady sedimentary condition with high sedimentation rates, thus rendering them ideal regions for exploring high-resolution paleo-sedimentary environment records. Since the sedimentary environment of the continental shelf is subject to the compound influence of multiple factors, the reconstruction of water salinity and temperature and comprehensive analysis of their response to global climate change remains challenging. Therefore, the present study characterized water salinity and temperature of the North Yellow Sea (NYS) using proxies, such as ratios of halogen elements of sediments and stable isotopic compositions of benthic foraminifera, and found the halogen elements of Cl in sediments was good proxy for water salinity. The evolutions of water salinity and temperature of the NYS for the past 3000 years were reconstructed, while the evolution stages and drivers of the sedimentary environment were explored. From approximately 3000 cal yr BP, the sea bottom salinity and temperature of the NYS were found to follow the same evolution trends predominantly consisting of the three stages: relatively low seawater salinity and temperature during 3000−2000 cal yr BP; relatively high seawater salinity and temperature during 2000−460 cal yr BP; and rapid changes of seawater salinity and temperature since 460 cal yr BP. The changes in seawater salinity and temperature of the NYS were largely driven by the East Asian winter monsoon (EAWM) as well as the influence of the Kuroshio Current. As the EAWM fluctuated, changes occurred in the flux of low temperature, low salinity coastal current water into the Yellow Sea, with concomitant changes in bottom temperature and salinity. Strengthening of the Kuroshio Current promoted the development of the Yellow Sea Warm Current, while the influx of warm, salty water into the Yellow Sea influenced the respective sea region. The abrupt global climate changes such as the “Little Ice Age” and the Medieval Warm Period first affected the East Asian monsoon, followed by the respective sea region.