Abstract: Diatoms play an important role in aquatic ecosystem, and it is widely used in water quality monitoring because of its widely distribution, short reproductive cycle and sensitivity to environmental changes. In order to establish the diatom index suitable for the ecological evaluation of water in China, the community structure and environmental characteristics of diatom in the main lakes in the lower reaches of the Yangtze River and the Qingyi River were investigated from August 2017 to August 2018. The relationship between diatom index and environmental factors was studied by Spearman correlation analysis, and the applicability of diatom index was analyzed by box-plot. The results showed that: (1) Based on the study of the relationship between diatoms and environmental factors in the lower reaches of the Yangtze River and Qingyi River Basin, the optimum and tolerant values of total phosphorus, chemical oxygen demand and total nitrogen of 114 diatoms to the environment were determined. CDI Index was established for water environment assessment of lakes and rivers. (2) Spearman correlation analysis showed that the CDI index was significantly correlated with the main environmental factors such as total phosphorus, chemical oxygen demand, total dissolved solids and total nitrogen in both rivers and lakes. (3) The Box-plot results show that the CDI index value increases gradually with the change of water quality gradient in both rivers and lakes, indicating CDI index can reflect the environmental quality of water.