China is still one of the countries dominated by thermal power generation. In order to generate more efficient, stable and clean power, it is necessary to evaluate thermal power generation units (TPGU). Firstly, a comprehensive evaluation index system for TPGU with 20 secondary indicators was established from four aspects: reliability indicators, economic indicators, technical supervision indicators, and major operating indicators. Secondly, the entropy weight method can be used to calculate the weight of each second-level index. Mahalanobis Distance improved Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) method is coupled with the Grey Relational Analysis (GRA), and the comprehensive evaluation values of 5 units (600MW) are respectively 0.4516, 0.5247, 0.3551, 0.5589 and 0.6168 from both vertical and horizontal dimensions. Finally, by comparing and analyzing this method with the above research methods, it is found that the results obtained by this method which re-establishes the coordinate system based on the data set are more accurate. In addition, this method can effectively evaluate the operation of TPGU, which is of great significance for cleaner production while generating electricity. In conclusion, some suggestions on clean production of TPGU are put forward, and the innovation points and limitations of this paper are pointed out.