Community characteristics of aquatic plant are important indicators for water quality. In order to understand the distribution characteristics of aquatic plants in aquatic ecosystem of the Beijing-Hangzhou Grand Canal ( Hangzhou section) , and to analyze the relationship between water quality and plant community, an investigation of the aquatic plants in five typical sites was made in this study. Species composition, biological diversity, quantity distribution and dominant species of aquatic plants in five sites were studied for ecological changes. Physicochemical factors such as temperature, pH value, transparency, dissolved oxygen and main elements of living were also analyzed. Based on the results, the distribution of phytoplankton diversity and environment factor correlations by multivariate statistical analysis were discussed. The trophic levels of these sites were assessed by using related biological standards. Results indicated that the diversity of aquatic plant mainly depends on the diversity of phytoplankton in the typical sites of the Beijing-Hangzhou Grand Canal. We observed and identified 35 genus algae, including advantage community of Hyalodiscus Ehrenberg and Melosira Agardh, which belonged to Bacillariophyta. According to the impact on the phytoplankton diversity and distribution, factors such as dissolved oxygen, transparency, water temperature, etc. had an obvious influence on the distribution of phytoplankton in the existing 6 environmental factors, while the influence of pH value was the highest. In terms of water quality eutrophication, site Tangxi Bridge and Maiyu Bridge showed a relatively lighter pollution, while site Yiqiao Bridge, Gujia Bridge and Gongchen Bridge showed a higher pollution, and the pollution of site Yiqiao Bridge was the most serious.