In order to realize the comprehensive health evaluation of the polar orbiting meteorological satellite application system, the comprehensive weight of the index value of the system to be evaluated is determined by combining the Analytic Hierarchy Process (AHP) of subjective analysis and the entropy weight (EW) of objective analysis, then the TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution) is used to rank the indexes of the system from multiple angles as the final evaluation result. In this paper, three polar orbiting meteorological satellites in five consecutive months are used to analyze the abnormal index samples in the actual operation system. The results show that this method considers many factors that affect the application system comprehensively, avoids the limitation of single criterion, and makes a comprehensive comparative analysis of the importance of each index, making the evaluation results more scientific and accurate, and it can be used as a method for the health evaluation of the polar orbiting meteorological satellite application system.