In order to understand the effect of emergency treatment developed by the laboratory on cyanobacteria of bloom in Najiang Reservoir and the water quality changes in the process of treatment, we studied the water quality and phytoplankton structure changes before, during and after the restoration of Nanjiang Reservoir. The results showed that the mass concentration of TN and TP decreased significantly after restoration, and the dominant species changed from the only dominant species Aphanizomenon flos-aquae before restoration to the after restoration:Lyngbya, Aphanizomenon flos-aquae, Oscillatoria princeps, Aphanocapsa and Synedra acus. The density of phytoplankton decreased from (39.2±0.52)×10⁷ cells/L in the early stage to (5.5±0.13)×10⁷ cells/L in the later stage of restoration;the biomass decreased from (24.64±3.25) mg/L before the restoration to (7.97±1.56) mg/L after restoration. Shannon-Wiener diversity index, Pielou evenness index and Margalef richness index were significantly lower in the early stage than in the middle stage (P < 0.05). Redundancy analysis (RDA) showed that water temperature (WT) and total phosphorus (TP) were the main environmental factors affecting phytoplankton, and total phosphorus (TP) was the key factor for outbreak of cyanobacteria bloom. The results above indicate that the emergency treatment can reduce the nutrient salt of nitrogen and phosphorus in water and reduce the chlorophyll content, and the effect of control on cyanobacteria bloom is significant in the short term.