Microalgal cultivation and harvesting are two main factors that restrict the development of microalgae. To help solve these two questions, flocculating bacteria and recycling culture medium were investigated in this study. Proteins in bacterial cells of Bacillus sp. y3 and y6 exhibited direct flocculation activities on Chlorella vulgaris cells. The recycling culture media after harvest of microalgal biomass by strain y3 and y6 could promote C. vulgaris growth. The determination of bacterial community confirmed that strain Bw in C. vulgaris phycosphere was the bacterial species that played the major promotion effect on microalgal growth. The functionary mechanism of strain y3 and y6 on microalgal growth was determined that they can influence C. vulgaris growth by changing the concentration of strain Bw to regulate algal ROS and antioxidant system response. The present study can provide effective research ideas and the application potential for the cultivation and harvesting of microalgae.