Benthic diatom indices developed in the Europe Union have been widely accepted as indicators of the trophic state and water quality in freshwater ecosystems. In China, most of the benthic diatom-based indices have not been widely tested or evaluated before. For this purpose, the water quality parameters and benthic diatoms community structures at 20 sample sites in the dish lake of Nanjishan Nature Reserve in Poyang Lake were investigated in this study and 18 widely-applied diatom indices were established. The statistical results indicated that most water quality parameters including Total Nitrogen (TN), Total Phosphorus (TP), ammonia nitrogen (NH4+), Chemical Oxygen Demand (COD) and Chlorophyll (Chl) were highly correlated with each other at a confidence level of 0.05. Water quality sampling sites from 8 lakes could be classified into 4 groups based on the integrated comprehensive scores using principal components analysis (PCA). Monitoring sites could also be divided into 4 groups based on clustering analysis with hierarchical methods for diatom dominant species in 20 sampling sites. According to the status of water ecological health recognition and box plot analysis in different water quality groups and diatom dominant species groups, only 3 diatom indices including the Biological Diatom Index (IBD), Specific Pollution Sensitivity Index (IPS) and Louis Leclercq Diatom Index (IDSE) demonstrated good evaluation suitability and good correlation within different water quality grades at the final stage. The above results revealed that IBD, IPS and IDSE were the most suitable diatom indices for the water quality evaluation of the dish lake in the Nanjishan Nature Reserve, Lake Poyang.