Abstract: Aquatic plant plays a crucial role in controlling the ecological conditions of crayfish (Procambarus clarkii) aquaculture. In order to clarify the path of different types of aquatic plants affecting crayfish culture performance, we examined the impacts of Hydrilla verticillata and Alternanthera philoxeroides on the growth and development performance of crayfish, and determined the intestinal natural diet composition by using high-throughput sequencing technology. H. verticillata and A. philoxeroides exhibited substantial water purifying properties, significantly increasing the dissolved oxygen (p<0.05), while decreasing the phosphate content, nitrite, ammonia and nitrate nitrogen contents (p<0.05). The growth indexes of H. verticillata and A. philoxeroides groups were significantly higher than those of the control group (p<0.05), whereas the former two groups showed no significant differences (p>0.05). The temperature, dissolved oxygen and pH had a greater effect on the growth performance of crayfish in H. verticillata and A. philoxeroides groups, while the nitrite and ammonia nitrogen had a stronger effect on the control group. The phytoplankton in the control group had significantly higher density and biomass than the aquatic plant groups (p<0.05), while A. philoxeroides group had a significantly higher abundance and diversity of plankton communities than the control group (p<0.05). The results of constrained principal axis analysis (db-RDA) reveal that the food content in crayfish intestines varied significantly among the groups (p<0.01). In summary, H. verticillata and A. philoxeroides can improve the aquaculture environment, promote the growth performance of crayfish, and enrich its food composition.