Shallow lake ecosystems are suffering from the extensive and intense anthropogenic disturbances, but little research has been conducted on harvesting macrophyte disturbance. In this study, a passage zoned harvesting project was conducted in August 2019 in Euryale ferox overgrown Lake Chenyao, and changes in phytoplankton communities in different treatment groups before and after harvesting of E. ferox were analyzed. A total of 72 species of 6 families, 47 genera and 72 genera of phytoplankton were identified during the study, including 63 species before and 71 species after harvest; the cell density and biomass of phytoplankton were higher after harvest than before, increasing by 39.78% and 5.09%, respectively. The harvest of E. ferox led to the change of phytoplankton community from cyanobacteria-green algae-diatom-cryptoalgae community to cyanobacteria-green algae-diatom community. The relative proportion of cyanobacteria was significantly higher than that before harvest (P<0.05), showed the increase of harmful cyanobacteria (Microcystis aeruginosa, Aphanizomenon flos-aquae, Oscillatoria tenuis, Dolicospermum circinale and Phormidium tenu). Harvesting also led to the transformation of diatom community from epiphytic to planktonic diatoms, with the decrease of Ulnaria acus and the increase of Aulacoseira granulata var. angustissima and Cyclotella meneghiniana. During E. ferox harvesting, there was no significant difference in the spatial and temporal distribution of phytoplankton community between the unharvested group and the river channel (P>0.05), but there were obvious differences in different stages after harvesting in the harvested group, and their cell density and biomass decreased gradually with the end of harvesting project. Correlation analysis between phytoplankton and environmental factors showed that aquatic vegetation coverage, total phosphorus, total nitrogen, dissolved oxygen and chlorophyll a concentration were the main environmental factors affecting the changes of phytoplankton cell density and biomass. Based on the water quality status of Lake Chenyao, this study concluded that harvesting E. ferox did not alleviate the eutrophication condition of shallow lakes, and the results of the study provided a theoretical basis for the management of aquatic vegetation in shallow lakes.