In order to solve the environmental pollution of aquaculture and improve the quality of aquatic products, a Multiple Aquatic-organisms Pond System was developed. The experimental system mainly included grass carp culture section, Chinese hairy crab culture section, snail and feeding-feed carp culture section as well as water treatment facilities. According to the biological habits of the aquaculture objects, the ponds were partitioned into several units, and the discharge of eutrophic substances was reduced through increasing the material circulation of nutrients in multiple aquaculture organisms of different ecological niches. In this study, a pilot scale system was constructed. The calculation model of water cycle process of the experimental system was established using CFD numerical calculation software. The flow characteristics of the whole system and the grass carp culture tank were studied, and the research of the water quality control performance was carried out. The results showed that the velocity value near the wall of grass carp culture tank was greater than that in the central area, which was conducive to the precipitation of particle waste and timely discharge. After the system was started for 300s, the flow state of water in the whole system tended to be stable, thus, the concentration of nutrients in each pond became well-distributed, which ensured the efficient circulation of substance and energy. The total nitrogen concentration was lower than 5mg / L and the total phosphorus concentration was less than 1mg / L, which met the discharge standard of freshwater aquaculture, but the decrease of COD was not significant. So, the structure of the Multiple Aquatic-organisms Pond System should be further improved to strengthen the treatment capacity of organic pollutants. This study provides a parameter reference for the design of Multiple Aquatic-organisms Pond System.