Abstract: Aiming at the deviation problem existing in the evaluation method of weighted average comprehensive nutritional status index TLI(Σ), when making by averaging the values of five evaluation indexes, including Chla, TP ,TN, SD and COD_Mn. The expressing efficacy of nutrient levels of different evaluation indicators under different lake conditions (nitrogen limitation, phosphorus limitation, nitrogen-phosphorus synergistic effect) was analyzed. The three indicators of Chla, TP and TN were selected as evaluation indicators, and the changed weight trophic level index (TLI_CW) evaluation method for comprehensive nutritional status index was obtained by comparing the apparent and potential nutritional status indexes. The method was applied in the Longhe River, a tributary of the Three Gorges Reservoir area. It showed that the TLI_CW method with variable weights was more prominent in describing the characteristics of nutritional status than the TLI(Σ) method. It was in the status of light eutrophication evaluated by TLI_CW method while in the status of mesotrophication by TLI(Σ) method. The TLI_CW mean value determined by the multi-lake response relationship reveals that Longhe River was one trohpic level higher than determined by the Longhe River response relationship. The eutrophication thresholds of the TP and TN determined by the Longhe River response relationship was of 2.75 and 3.00 times respectively of multi-lake response relationship, indicating that there was a clear over-protection problem when the multi-lake response relationship was used in the eutrophication evaluation of Longhe River.