The invention particularly relates to a method for establishing an improved functional decomposition-based secondary system risk quantification model. The method comprises the following steps: firstly, decomposing function-involved hardware and software, abstracting the hardware and software to logical nodes and logical connections, obtaining a functional diagram; then analyzing the failure probability of the logical nodes and the logical connections; finally, solving a path with the maximum failure probability, wherein the end of the path in the functional diagram is an end node, and the failure probability of the path is the failure probability of the function. The invention provides a calculation method of functional failure probability according to an information flow directed graph; the method determines the functional failure probability through searching for the path with the maximum failure probability in the directed graph.