This paper studied the removal effect of nitrogen and phosphorus in eutrophic waters with three kinds of co-immobilized bacteria-algae (bacteria; activated sludge, algae: Chlorella, Pediastrum and Scenedesmus Obliquus) systems through setting up multiple immobilization systems, and the processing effects of eutrophic waters of different degree (five concentrations). The results showed that, in treatment of eutrophic waters, co-immobilized bacteria-alga system has a lot of advantages in the role of removing nitrogen and phosphorus by embedded on the same carrier. The best ratios of co.-immobilized bacteria-algae of three kinds of algae are: Chlorella; bacterial = 1:1, Pediastrum,; bacterial = 2' 1, and Scenedesmus obliquus; bacterial = 1:1, the maximum cumulative removal rates of TN are 39.03%,36.31% and 34. 34%, and the maximum cumulative removal rates of PO3-4-P are 88.55%,91. 73% and 86.00%. Under the optimal condition, the removal effects of nitrogen and phosphorus in different degrees of eutrophic waters were also studied. The results show that, in the lower concentration of eutrophic waters, the system with Pediastrum; bacterial = 2-1 and Scenedesmus obliquus; bacterial = 1:1 has excellent performance of nitrogen and phosphorus removal; while the system with Chlorella; bacterial = 1:1 has good purifying effects in different concentrations of eutrophic waters. In weighty eutrophic waters, the maximum cumulative removal rates of TN,NH4+-N and PO3-4 - P by the system of Chlorella: bacterial =1=1 are 98. 82%, 99.34% and 94.01%. This result could meet Class I surface water environment quality standard.