The inhibiting effects of immobilized photosynthetic bacteria on Microcystis aeruginosa were investigated in this study. First, through comparison of five immobilization methods and their features, the optimal immobilization method was determined. Then, photosynthetic bacteria and Microcystis aeruginosa were co-cultured through laboratory experiments. After the experiments, the impacts of immobilized photosynthetic bacteria and mobile photosynthetic bacteria on the growth of Microcystis aeruginosa were studied, and the optimal dosage of immobilized photosynthetic bacteria was determined. The study results show that the optimal method for immobilization of photosynthetic bacteria was to mix zeolites, calcium carbonate, and sodium alginate. The immobilized photosynthetic bacteria had a significant inhibiting effect on Microcystis aeruginosa, with an inhibition rate of 83.55%, while the mobile photosynthetic bacteria, at the same amount, had an inhibition rate of only 26.81%. The optimal dosage of immobilized photosynthetic bacteria was 36 g/ L.