This study aimed to elucidate the dynamics of phytoplankton community structure in Litopenaeus vannamei culture ponds, compare them with those in surrounding waters, and explore the correlation between phytoplankton and environmental factors. Samples were collected from the aquaculture ponds and the adjacent river of a L. vannamei farm in Fengxian District, Shanghai. Multivariate analysis was employed to examine the relationships between phytoplankton and environmental parameters. The study identified 67 genera across 7 phyla in the ponds, with Chlorophyta predominating at 51%. The dominant genera included 28 genera from 5 phyla, with Chlorella being the most prevalent in Bacillariophyta (F=1.0). The overall average phytoplankton density was 1.09×10⁷ ind/L, with Chlorophyta, Cyanophyta and Bacillariophyta contributing 47%, 30% and 11%, respectively. Positive correlation were observed between the phytoplankton community structure and levels of total nitrogen (TN), total phosphorus (TP) and chemical oxygen demand (COD). In the adjacent river, 7 phyla and 56 genera were detected with Chlorophyta account for 46%, among which 6 phyla and 26 genera were dominant with Cryptococcus and Cryptomonas being the dominant genera. The average phytoplankton density was 1.18×10⁵ ind/L, with Cryptophyta, Bacillariophyta and Chlorophyta comprising 46%, 27% and 13%, respectively. The river's phytoplankton structure was primarily influenced by the abundance of colonies and rotifers. The pond's phytoplankton density was significantly higher and more complex than that of the river, with Microcystis blooms posing a risk to the healthy of L. vannamei during September and October. This necessitates close monitoring of TN, TP, and organic matter levels. The study thus highlights the differences in phytoplankton community structure between shrimp culture system under artificial intervention and natural ecosystem.