The technique of combining two or more kinds of organisms to treat eutrophic water in ecological restoration has drawn much attention. In this paper, Daphnia magna and Vallisneria natans were used as the representatives of the zooplankton and submerged macrophytes to establish the combined system of daphnia-grass, the treatment of Vallisneria natans was used as the control group, and the eutrophic water as the blank group. Then we researched the process of water quality indicators, sediment indicators and aquatic biomass changes.The results showed that the quality indexes of water and sediment in the system were superior to that of the bitter Vallisneria natans group. The final removal rates of total nitrogen, total phosphorus and ammonia nitrogen were 87%, 88% and 96%, and the maximum removal rates were 70%,70% and 86%respectively. The removal rate of total nitrogen in sediment was 39% and the removal rate of total phosphorus was 38%. After 27 days of water clearing, the growth rate of Vallisneria natans reached 740%. In the control group, the final removal rates of total nitrogen, total phosphorus and ammonia nitrogen were 35%, 33% and 57%, and the maximum removal rates were 35%, 30% and 57% respectively, and the removal rate of the total nitrogen and total phosphorus was 40% and 32%, respectively. The water was not clear enough to see the bottom after 48 days, and the growth rate of Vallisneria natans was 470%.Therefore, Daphnia magna promoted the settlement of suspended solids, which is conducive to the growth of Vallisneria natans and the stability of the system. The ability of daphnia-grass system to deal with eutrophic water is greater than single aquatic systems, and it can speed up the transparency of water, achieve a higher growth rate of Vallisneria natans and is easier to maintain the stability. All in all, the experimental results provide reference for guiding the ecological restoration engineering practice.