The diatom index has been widely used in the evaluation of water ecological quality, but the applicability of the diatom index often varies in different study areas. The accuracy of the evaluation results depends on the applicability of the diatom index, especially when it is not applied to the place where it is created. In order to screen out the diatom index suitable for the evaluation of the water ecological quality of Tangwang River in northeast China, and to identify the factors affecting the accuracy of the diatom index, the community structure and water environment characteristics of 24 sample sites were investigated in Tangwang River in August 2018, and 18 diatom indices were calculated. The discriminative ability of diatom indices was analyzed using the box plot method, and the factors affecting the accuracy of the diatom index were identified by combining Pearson and Spearman correlation analyses. The results show that the discriminability of the Biological Diatom Index (BDI), Specific Pollution Sensitivity Index (IPS), Idse Leclercq (IDSE), Indice Diatomique Artois Picardie (IDAP), Diatom Eutrophication Pollution Index (EPI-D), Trophic Index (Rott TI), European Economic Community Index (CEE), and Watanabe Index (WAT) was the strongest, which could reasonably distinguish the reference group from the lightly damaged group. In general, the water ecological condition of Tangwang River Basin is good in the wet season, and the water ecological quality of about 80% of the sample sites was “moderate” or better. The main factors affecting the evaluation accuracy of the diatom index in Tangwang River Basin are the correlation strength between the diatom index and habitat quality, organic pollution, and nutrients. The coverage of diatom index species had no significant effect on the accuracy of evaluation. In order to reasonably evaluate the aquatic ecological status, it is recommended to use the diatom index, which has a good correlation with the environmental factors in the study area, or to establish a new diatom index based on the diatom community and environmental factors in the study area.