Many reports have demonstrated that the removal of aquaculture purse seine is conducive to the restoration of aquatic vegetation and the improvement in water quality, but less attention has been paid to the effects on phytoplankton. This paper addressed the response of phytoplankton community structure to aquatic vegetation restoration after purse seine removal in Caizi Lakes. The results showed that the average dissolved oxygen (from 7.43 ± 0.25 mg/L to 9.12 ± 0.49 mg/L) and Secchi depth (from 28.40 ± 6.20 cm to 47.61 ± 14.62 cm) in the water column of the Caizi Lakes increased after the restoration of aquatic vegetation, while the average concentrations of total nitrogen (from 2.00 ± 0.16 mg/L to 1.34 ± 0.18 mg/L) and total phosphorus (from 0.15 ± 0.02 mg/L to 0.06 ± 0.01 mg/L) decreased. After the restoration of the aquatic vegetation, the cell density of phytoplankton declined from 21.04 ± 4.57 × 106 cells/L to 12.74 ± 3.63 × 106 cells/L, and the biomass fell from 18.13 ± 3.57 mg/L to 9.72 ± 2.55 mg/L. We also observed that Shannon–Wiener diversity, Margalef and Pielou indices of phytoplankton surged by 66.50%, 46.20% and 84.68%, respectively. Because this study demonstrated that aquatic vegetation could alleviate the eutrophication, it can provide guidance for the restoration and protection of the aquatic ecosystem.