Water resource is a major limitation of human survival and development. Water security assessment is an important task in the environmental protection and control of water. The solution to assess the grade of water security in the Yellow River Basin is to study based on the theory of matter element of extension method. Considering the factors of water resources, water environment and social economic aspects, the assessment index system of water security is established . Based on the defining of assessment level, water security assessment based on matter element model is developed exerted both qualitative and quantitative analysis. According to the calculation of correlation degree in the matter element model, the assessment result is represented by the quantitative data that can reflect water security situation in the Yellow River Basin briefly.The result shows that: water security in Qinghai and Sichuan province is in security level, that in Henan province is in the relative security level, that in Shaanxi and Shandong province is in the security threshold level, that in Shanxi province is in the relative insecurity level and that in Gansu, Ningxia and Inner Mongolia province is in insecurity level. The result of matter element model is scientific and reasonable, simple and easy, and can meet the factual data. matter element model can be used in water security assessment and can reveal the complementary information of every single assessment index.