The risk assessment is an important task in operational management. Since secondary system of substation(SSOS) is an important part to ensure the safe operation of the substation, close attention is needed to its operation risk causing power loss. According to past research, the difficulties of its risk assessment include complex relationship of secondary devices, and risk analysis of its impact on primary devices. Therefore, the graph theory and risk contagion model are introduced to deal with these difficulties. The secondary system risk assessment is decomposed into two parts. One is its own risk (secondary risk), another one is focused on the quantification of the corresponding primary risk (primary risk). The risk assessment model including the basic elements definition, constructing risk contagion network, and composing correlation matrix, is established. Then, a set of risk indexes for SSOS is presented according to the needs of different operation departments. Finally, an instance secondary system of an intelligent substation is modeling to test the validity of proposed model. The result supports the usefulness of the risk assessment.