In order to understand the direct and indirect effects of Daphnia magna on phytoplankton composition in unfiltered raw water that contained in situ zooplankton, and which densities of Daphnia magna will control phytoplankton effectively, we carried out a simulated experiment in May 2016. The experiment had one control (C0) group and four treatment groups C1, C2, C3 and C4. We added D. magna at five different levels (0, 5, 15, 25 and 50 ind./L). Each treatment had triplicates and lasted for 10 days. The results indicated that both low (C1 and C2) and high (C3 and C4) densities of D. magna could suppressed phytoplankton abundance, but the latter is more effective. Daphnia magna prefer grazing green algae and phytoplankton whose particle size is between 20 μm and 30 μm. Moreover, it can suppress abundance of Bosminopsis deitersi, Diaphanosoma leuchtenbergianum, Cyclops, rotifers and protozoa, and the higher the density is, the stronger inhibitory effect (except protozoa), affecting phytoplankton community indirectly. Additionally, we found addition of D. magna at 25 ind/L performed best, which reduced the abundance of algae dramatically, fell by 75.1%, on the fourth day.