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Recent years, Chinese people pay much attention on the health security system. We make efforts to help the government to analyze the health security system of all parts of the country. In our paper, we utilize two models, Factor Analysis (FA) and Gray Relation Analysis (GRA), to evaluate the health security system from both time-vertical and place-horizontal aspects. FA is a fantastic model when objects are evaluated by multi-index. It simplifies the preliminary selection index so that via FA, we can achieve the dimension reduction of index processing. Based on the assessment results, we can conclude that health security system presents a steady upward trend. Then we propose another evaluation model GRA to analyze the influence factors of health security system among all parts of the country. GRA catch the important factors according to the key relationship among various indexes especially when there are not enough data. We obtain the rank about health security system of all parts of the country at last.