The structure of plankton community and water environment features in ponds under partition cluster clean aquaculture were studied by using the traditional model pond as control. Through collecting water samples and monitoring water chemistry index, some indicators include phytoplankton species, density, biomass and so on were identified. The differences between cluster aquaculture model and traditional aquaculture model in phytoplankton community structure and water chemistry index were analyzed using related statistical methods. The results indicated that the TN concentration both inside and outside of cages set in the new model pond are 1.22 mg/L and 1.31 mg/L, respectively. TP concentration are 0.169 mg/L and 0.170 mg/L, respectively. However, TN and TP concentration were 1.76 mg/L and 0.689 mg/L, respectively in traditional aquaculture ponds. A total of 6 phylum and 169 species of phytoplankton were detected, and green algae was the dominant taxonomy. The next is Cyanophyta and Baccillariophyta. And the dominant species are also concentrated in the three species. Phytoplankton biomass of intensive aquaculture area was 24.54 mg/L, diversity index was 2.52, and biomass and diversity index of clean area was 23.51 mg/L and 2.47, respectively. A total of 183 species of zooplankton were identified in the survey area, and the maximum dominant species occurred in rotifer. The next is Protozoa, and the least are Cladocera and Copepoda. Zooplankton biomass of intensive aquaculture area was 3.53 mg/L, diversity index was 1.82. Biomass and diversity index of clean area were 2.95 mg/L and 1.86, respectively. Biomass of phytoplankton and zooplankton in traditional aquaculture ponds were 49.12 mg/L and 0.53 mg/L, respectively. And their diversity index were 2.06 and 1.79, respectively. Compared with the traditional model, at the new model pond, stool accumulation was reduced, TN and TP concentration were decreased, the decline in the proportion of cyanobacteria, phytoplankton biomass decreased, the increase in zooplankton biomass and improve the biodiversity index and water environment has been improved to some extent. And provide a better living environment for farmed fish. The reslut showed that the state of experiment pond is higher than traditional pond. At the same time, contrast with production of two aquaculture model. It indicated that the fishes survival rate increased in cluster model, and feeding efficiency significantly increased, the production significantly increased relative to the traditional aquaculture model and rate of return on investment is very large. Last, the partition cluster clean aquaculture model have a significant help to aquaculture development and benefit, and it is suitable for promotion.