Secondary system has become increasingly important in the safe operation of power systems. How to assess the impact of the secondary system is a difficult problem for power system security and risk assessment. According to the protection relay configuration in substation, the topology model is proposed with the consideration of both function decomposition and associated relationships of secondary devices. Considering topological relationship between secondary devices and protection functions, a protection system failure probability computing model is derived, which is composed of failure probability of each secondary device. Based on different effects on primary system operation of the protection relay failures, mistake action and rejecting action, risk assessment and evaluation processes which integrated primary system and secondary system is constructed. Finally, the model of primary and secondary system based on IEC 61970 CIM is established, including primary and secondary components models, the computational interaction model and the event consequence model. The risk calculation process is described in detail, especially the data sources and key steps.