Dredging is a common measure for ecological restoration in reservoirs, but it may also affect phytoplankton community structure. Human Reservoir, an important drinking water source in Wenling City, has experienced blooms of Raphidiopsis raciborskii in recent years. To reduce internal nutrient loading and improve water quality, whole-reservoir dredging was conducted from February to September 2024. To evaluate the effects of dredging on the phytoplankton community, this study monitored R. raciborskii blooms in Human Reservoir from October 2023 to September 2025. Phytoplankton community composition, diversity, niche, and their relationships with environmental factors were analyzed across different periods defined by bloom stages and the dredging process. The results showed that nutrient concentrations decreased significantly after dredging. A total of 55 phytoplankton genera belonging to seven phyla were identified during the monitoring period. Total phytoplankton cell abundance declined markedly during dredging but increased again after dredging. The dominant cyanobacterial taxa were Raphidiopsis and Pseudanabaena, showing a temporal succession from Raphidiopsis to Pseudanabaena. The abundance of R. raciborskii was highest before dredging, reaching 2.56×10?cells/L, decreased during dredging, and increased again after dredging. Phytoplankton diversity was relatively low before dredging but increased markedly after dredging. Redundancy analysis indicated that the phytoplankton community was positively correlated with nutrient concentrations before dredging, whereas this relationship weakened after dredging. The random forest model showed that bloom stage and dredging process were the key factors influencing phytoplankton community structure, followed by ammonium nitrogen. The niche breadth of R. raciborskii narrowed during dredging and widened after dredging. Multivariate homogeneity of group dispersions (PERMDISP) tests indicated that the phytoplankton community structure gradually returned to its pre-dredging state within one year after dredging. These results suggest that dredging can improve water quality and suppress R. raciborskii blooms in the short term; however, its effect is limited in duration, as the phytoplankton community gradually recovers and the bloom rapidly rebounds after dredging.