In order to identify vulnerable points in complex system roundly and assess its vulnerability scientifically, to improve the insufficiency of the pure topological methods, an analysis method integrated complex network theories and effectiveness assessment technologies was proposed, which considers both the topological and non-topological factors of vulnerability. Based on centricity measurements of complex network, a generalized indicators method was used for topological vulnerability analysis. Referring to the probability risk assessment theory, non-topological vulnerability was analyzed from susceptibility and brittleness. Then the final vulnerability results were integrated from the former two results. The demonstration results show that there is an intersection set but also some differences between topological and non-topological analysis. These two aspects of vulnerability are correlative and complementary close, they both contribute to the screening of critical points and links in a complex system, and compared to purely topological study, conclusions from integrated analysis were more comprehensive.