Phosphorus is a key nutrient element in lake ecosystems and a primary limiting factor of primary productivity. The forms and concentrations of phosphorus in water significantly influence phytoplankton community structure. To explore the characteristics of phosphorus fractions in a typical shallow lake of the middle and lower reaches of the Yangtze River—Lake Changhu—and their effects on phytoplankton community structure, and to provide a scientific basis for ecological restoration and precise management of Lake Changhu, we systematically sampled phosphorus fractions, other environmental variables, and phytoplankton communities at 10 sampling sites across the lake in March, May, September, and December 2024. Results showed that the annual mean concentration of total phosphorus (TP) in Lake Changhu was 0.117 mg/L, with a seasonal pattern of September > March > May > December and a decreasing spatial gradient from west to east. Overall, dissolved total phosphorus (DTP; mean value of 0.060 mg/L) contributed slightly more to TP than particulate phosphorus (PP; mean value of 0.056 mg/L). Specifically, PP dominated in March; in May, PP slightly exceeded DTP; whereas DTP predominated in September and December. Among dissolved phosphorus fractions, dissolved organic phosphorus (DOP) was dominant in September, while dissolved inorganic phosphorus (DIP) was dominant in December. The concentration of DOP in September was significantly higher than in other months. The dominant phytoplankton groups in Lake Changhu were Cyanophyta, Chlorophyta, Bacillariophyta, and Cryptophyta. Non-metric multidimensional scaling (NMDS) and permutational multivariate analysis of variance (PERMANOVA) showed significant differences in phytoplankton community structure among sampling months, exhibiting clear seasonal succession patterns. From March to December, the phytoplankton community transitioned from Bacillariophyta + Cryptophyta + Chlorophyta→Cyanophyta + Chlorophyta→Cyanophyta→Cryptophyta + Bacillariophyta + Cyanophyta + Chlorophyta. Specifically, Cyclotella sp. (Bacillariophyta), Merismopedia minima (Cyanophyta), and Komma caudata (Cryptophyta) were the dominant species in March, May, and December, respectively. Microcystis spp. (Cyanophyta), a bloom-forming cyanobacterium, dominated in September and was also a dominant species in May. Redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) results indicated that DOP, water temperature, DTP, and suspended solids significantly influenced phytoplankton community structure, with phosphorus fractions exerting significant direct effects. Among these, DOP exhibited the strongest positive influence, particularly affecting the abundance of Microcystis spp.. In summary, our findings highlight that phosphorus fractions significantly influence the phytoplankton community structure in Lake Changhu and underscore the necessity to quantitatively assess the ecological risks of different phosphorus fractions, especially DOP, in eutrophic shallow lakes.