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This paper discusses the long-term variation in the salinity of the Southern Yellow Sea Cold Water Mass (SYSCWM) and examines factors influencing the SYSCWM based on hydrographic datasets of the China National Standard section and the Korea Oceanographic Data Center. The mean salinity at the center of the SYSCWM showed a decreasing long-term trend. In empirical orthogonal function (EOF) analysis, the second EOF mode showed a similar long-term trend. The mean salinity of the center of the SYSCWM was related to the intrusion of saline water from the Yellow Sea Warm Current (YSWC), the salinity of the source area of the YSWC, the evaporation minus precipitation (E–P) flux, and discharge from the Changjiang River. The decreasing salinity trend to the southwest of Cheju Island produced a freshening trend in the YSWC, resulting in a reduction in the salinity of the SYSCWM. The freshening trends of the water from the northwest Pacific and the South China Sea were seen as the reason for the decreasing salinity trend from the intrusion of water into the Yellow Sea (YS). The freshwater flux influenced the surface salinity and was brought to deep layers by strong mixing in winter. The mean E–P flux signal and Changjiang River discharge signal lagged the first principal component of the SYSCWM by approximately 5 months.