The occurrence of nano-plastics (NPs) in the aquatic environment has become a global environmental problem. As one of the important primary consumers in freshwater, Daphnia magna is widely used in the biological manipulation and restoration of eutrophic water, while the potential influence of NPs on the feeding behavior of Daphnia magna remains unclear. In the current study, we performed a 21-day experiment and investigated the effect of polystyrene nanoplastics (PSNPs, with size of 1000 nm) exposure on the grazing behavior and physiological response of Daphnia magna toward toxic Microcystis aeruginosa and Scenedesmus oblique. The results showed that in the treatment with toxic Microcystis aeruginosa, the developmental and reproductive toxicity of Daphnia magna were the most obvious. Compared with the control group (feed with Scenedesmus obliquus), the activity of superoxide dismutase (SOD) and the content of malondialdehyde (MDA) in the Daphnia magna that feed with Microcystis aeruginosa were 3.97 and 4.55 times higher. Meanwhile, the total number of oviposition and body length were decreased by 73% and 13%, respectively. And the filtration rate of Daphnia magna to toxic Microcystis aeruginosa increased with time. Upon exposure to 3.56 mg/L PSNPs, the grazing ability of Daphnia magna was significantly reduced in all treatments, and the feeding rate of Daphnia magna to Scenedesmus oblique was decreased by 32% when PSNPs were added. In the mixed feeding systems containing toxic Microcystis aeruginosa and Scenedesmus obliquus, exposure to PSNPs reduced the feeding rate of toxic Microcystis aeruginosa by 66%, and thereby alleviated the developmental and reproductive toxicity towards Daphnia magna, however, inhibited the reduction of Microcystis aeruginosa biomass.