Based on historical data from 1976 to 2019, the effects of anthropogenic activities on long-term changes in nutrients and their ecological effects in the South Yellow Sea were investigated. The dissolved inorganic nitrogen (DIN) concentrations increased continuously from 1990 until the mid-2000s, followed by a shift from an upward trend to a downward trend. The phosphate (PO4-P) and silicate (SiO3-Si) concentrations also showed obvious interannual variations throughout the study period. The concentrations of DIN, PO4-P and SiO3-Si have decreased significantly in recent decade and more. These changes mainly resulted from the reduction in terrestrial input, while the main reason for the decrease in DIN and PO4-P concentrations is the reduction in anthropogenic input. The long-term nutrient changes in the South Yellow Sea have potential ecological impacts on green tide features.