The aerobic formers of Exiguobacterium and Bacillus licheniformis were screened to construct a Chlorella-bacteria consortium for the piggery wastewater treatment. The optimal consortia of Chlorella-Exiguobacterium (C.v-E.x) and Chlorella-Exiguobacterium/Bacillus licheniformis (C.v-E.x/B.l) were designated to purify wastewater scaled-up in a column photobioreactor. The results showed that the rates of contaminant removal and cell growth of the Chlorella-bacteria consortium were all higher than those of the axenic Chlorella system and pure bacterial system. The C.v-E.x consortium had the best purification effect, and the concentrations of total phosphorus (TP) and ammonia nitrogen (NH4+-N) were reduced to 1.8 mg L−1 and 35.0 mg L−1 after 12 days, respectively. The final removal rates of total nitrogen (TN), TP, NH4+-N, and chemical oxygen demand (COD) were 78.3%, 87.2%, 84.4%, and 86.3%, respectively, and these levels were below the wastewater discharge standard (GB18596-2001, China). The mutualistic interactions between Chlorella and its coculture bacteria were explored by detecting total inorganic carbon (TIC), net photosynthetic activity (NPA), dissolved oxygen (DO), pH, and nitrogen-related enzyme activity. The results showed that the C.v-E.x consortium had a higher NPA (70.8% increase), DO concentration (172.4% increase), and TIC concentration (71.0% increase) and maintained a low pH 9.3 compared with the axenic C. vulgaris system. Therefore, the synergistic interactions of cell growth promotion and the exchange of carbon and oxygen between microalgae and bacteria were identified. The detection of nitrogen-related enzymatic activities in the photosynthesis pathway of Chlorella demonstrated that Exiguobacterium obviously improved the activities of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamate synthetase (GOGAT) by 94.2%, 57.5%, 58.6%, and 79.4%, respectively. This result indicated that cocultured bacteria might secrete some metabolites as enzyme activators, and there was a synergistic mechanism in the enzymology between microalgae and bacteria. The research provides a reference for the wastewater resourceful treatment by microalgae-bacteria consortia.