The effects of light intensity, bacteria to algae ratio, and initial ammonia nitrogen concentration on the removal of ammonia nitrogen were investigated in the Chlorella-bacteria agent system. The parameters were optimized by response surface analysis. The pathway of NH3-N removal and the mechanism of algae-bacteria symbiosis mechanism were discussed. The results showed that when the light intensity was 4 000 lux, the bacteria-to-algae ratio was 3 ∶ 1 and the initial ammonia concentration was 50 mg·L-1, the ammonia removal (%) reached the highest (94.92%) . The factors ranked from high influence to low influence on the removal of ammonia nitrogen was light intensity > initial ammonia nitrogen concentration > bacteria to algae ratio. Under the optimal parameters of light intensity of 4 700 lux,bacteria algae ratio of 3 ∶ 1 and initial ammonia nitrogen concentration of 50 mg·L-1, the measured and predicted ammonia nitrogen removal (%) were 87.96% and 87.31%, respectively. When the ammonia nitrogen concentration was 50 mg · L-1, the microalgae and the bacteria contributed 75.86% and 17.50% of ammonia nitrogen removal, respectively. The bacteria maintained the pH balance of the system and the EPS, as a key medium for the mutual beneficial symbiosis of algae andbacteria, maintained the virtuous cycle of the system. The key bacteria genera which was mutually beneficial symbiosis with microalgae could maintain relative stable in the system.