To optimize aquatic ecological structure and to regulate water quality, Chlorella vulgaris and effective microorganism were added to Exopalaemon carinicauda pond and fishponds. The results showed that after adding Chlorella vulgaris to the shrimp pond and fishpond, Chlorella vulgaris turned into a dominant species, and its amount was 16.92 and 4.76 times of CK. The zooplankton biomass reached to 4.32 mg.L-1 and 2.84 mg.L-1, increasing by 19.3% and 2.5%, compared with CK, respectively. Rhodospirillaceae, photosynthetic bacteria and yeast saccharomycete in the ponds could obviously change the composition, number, ratio, and biomass of the plankton (phytoplankton and zooplankton), and adjust aquatic chemical environment. The treatment of "Saccharomycete + Nitrifying bacteria" decreased the concentrations of NH4+ obviously, which was only 44% of CK. The BOD and COD in shrimp ponds were only 56.5% and 38.4% of CK. The treatment could increase the dissolved oxygen and primary production in the pond.