Submerged macrophytes play an important role in maintaining clear water in shallow eutrophic lakes. The submerged macrophytes exert strong influence on the phytoplankton by several mechanisms, including the excretion of allelopathic substances. However, the allelopathic substances from various submerged macrophytes are not completely the same. Allelopathy of different submerged macrophytes may have various effects on the biomass and community structure of natural plankton. This paper investigated the allelopathic effects of three species of submerged macrophytes, Vallisneria spiralis, Ceratophyllum demersum, and Myriophyllum spicatum, on the biomass and community structure of the phytoplankton collected from the west part of Hangzhou West Lake wetland, using mesocosms under controlled environmental factors, such as light and nutrients. The changes in the phytoplankton density, chlorophyll-a content, phytoplankton community composition, and Shannon-Weiner Index (H) were monitored. The results showed that the total phytoplankton density and chlorophyll-a content were significantly reduced, and that the phytoplankton community structure also changed in all three co-culture systems. At the end of the experiment, the total biomass of algae (cell density) was 37.06%, 78.37%, and 83.40% lower than the initial values of each system. However, the phytoplantkton-inhibitory ratios were not significantly different among the three species of submerged marcophytes (P > 0.05). The dominant algal genera in the control group were Pediastrum and Crucigenia; in the V. Spiralis group were Chlorococcum and Volvox; in the C. demersum group were Chlorella and Pediastrum; in the M. spicatum groups was Chlorococcum. Scenedesmus exhibited less sensitivity to the allelopathic substances from the three submerged macrophytes. The highest phytoplankton species richness was observed in the M. spicatum group. The Shannon-Weiner Index (H) was 2.76, 2.06, and 0.72 for the V. spiralis, C. demersum, and M. spicatum groups, respectively. Furthermore, the phytoplankton biodiversity index (H) of the M. spicatum group is significantly higher than that of the V. spiralis group (P < 0.05).