Aquatic plants are important components of freshwater ecosystems and constitute a dominant actor in many shallow lakes. Planting aquatic plant, especially for submerged macrophytes, is one of the most important ecological restoration methods widely used in damaged shallow freshwater bodies. However, previously studies have mainly focused on the effects of macrophyte richness on biomass and water quality. Little is known about the effect of different assemblages with various growth form submerged macrophyte on biomass accumulation and water purification. In this study, three different growth form submerged plants, Vallisneria natans, Hydrilla verticillata and Myriophyllum spicatum, which are commonly used in water ecological restoration in China, were selected to test the effect of different growth form submerged macrophyte assemblages on water quality and nutrients removal rate. Our results showed that all different growth form assemblages have obvious purification effects on total nitrogen, total phosphorus and ammonia nitrogen, and higher purification effects were observed in the early and middle stage of the experiment. From different combinations, one and two growth form combinations have higher biomass accumulation and higher total nitrogen removal efficiency than three growth form combinations. Pearson correlation analysis showed that the pH, and DO in the experimental system were significantly positively correlated with the total biomass, and the concentrations of total nitrogen, total phosphorus and ammonia nitrogen were significantly negatively correlated with the total biomass. Our results suggest that in order to get the best restoration results, we need to take various factors into consideration during the process of ecological restoration, including different life form and growth form aquatic plant assemblages, harvesting aquatic macrophytes, etc.