Abstract: A green, healthy and ecological aquaculture model represents the ultimate objective within the field. In this study, we investigated the ecological aquaculture model of Odontobutis obscura by comparing and analyzing the results of four water quality, plankton and zoobenthos samplings in two different cultivation systems: pond and rice-fish culture. The results showed that there were no significant differences in water temperature, pH and total phosphorus between the two culture modes. However, the rice-fish culture consistently exhibited higher levels of dissolved oxygen compared to pond culture. The concentrations of ammonia nitrogen, nitrite nitrogen and nitrate nitrogen generally showed a decreasing trend, while the total nitrogen content continued to increase. The chlorophyll-a content was always significantly higher in the pond culture than that in rice-fish culture. In both cultivation systems, 6 phytoplankton families and 40 phytoplankton genera were detected, with 8 phytoplankton species unique to each system. The phytoplankton density and biomass were the highest during the tillering stage, followed by the flowering stage. Zooplankton were detected into 3 major groups, encompassing 21 genera and 41 species, with Rotifera dominating in both modes. The highest zooplankton density and biomass of both modes were observed during the stem elongation stage, with the culture ponds consistently surpassing the rice-fish culture in zooplankton density and biomass, except during the ripening stage. The study identified a total of 9 benthic species (genera) were detected, and the common species was Branchiura sp.. The number of zoobenthic species and their quantities in both pond and rice-fish culture decreased as the rice crop grew. In summary, the results demonstrated that compared with the pond culture, the rice-fish culture model can purify the water quality to a certain extent and maintain the ecological balance in the paddy field by controlling the growth of plankton.