Abstract: According to the partition method, the water quality and ecological monitoring data of the Yangtze River Estuary from 2016 to 2021 were used to analyze the spatiotemporal characteristics of nutrients and its influencing factors. The study area was divided into entrance zone (S<5‰), estuary (5‰<S<25‰) and seawater zone (S>25‰). The results show that: (1) The concentrations of DIN and PO₄-P showed fluctuating downward trends, and SiO₃-Si showed fluctuating upward trends from 2016 to 2021. The DIN concentration of mainly showed a trend of spring > summer > autumn, while PO₄-P and SiO₃-Si were the opposite. (2) Affected by the freshwater of the Yangtze River, the concentrations of DIN and SiO₃-Si showed a trend of entrance zone > estuary > seawater zone, while the PO₄-P concentration was highest in the estuary. The area with high PO₄-P concentration was usually located near the maximum turbidity zone. The growth and reproduction of phytoplankton was one of the most important reasons for nutrients. (3) The distribution of nutrients in the Yangtze River Estuary was uneven, with N/P and Si/P much larger than 16∶1 and Si/N close to 1. Phosphorus was a potential limiting factor for phytoplankton. The relatively high value area of chlorophyll a was mainly limited by P, and N/P and Si/P were generally high. The absorption of organisms will exacerbate the degree of P limitation, suggesting that phytoplankton have an important impact on the nutrient structure. The research shows that the distribution of nutrients in the Yangtze River Estuary has obvious regularity, and the freshwater of the Yangtze River has an important influence on the spatial distribution of nutrients. The absorption of phytoplankton was one of the influence factors of nutrient structure. The research results can provide a basis for the improvement of the ecological environment of the Yangtze River Estuary.