The stochastic dynamic behavior of power secondary system is opaque and difficult to visualize, which obviously hinders the control of the uncertainties brought by strong dependence on information and communication technologies in new power systems. In this paper, methods for steady-state analysis, static security analysis, and transient analysis of power secondary systems, are proposed for the first time. First, a smart substation secondary system with complex functional descriptions is taken as the research object. A simulation tool for the secondary system of intelligent substations is developed and integrated into general network simulation software, which faithfully simulates the entire process of digital information transmission, flow, and processing in the secondary system. Combined with the device-level simulation tester, system-level path tracking and delay recording technology, scenario-level action characteristic display technology, and simulation acceleration technology proposed in this paper, and taking an actual intelligent substation engineering project as a case study, the steady-state analysis, static security analysis, and transient analysis of the power secondary system are realized under network transmission steady-state scenarios, secondary component (partial) failure scenarios, and circuit breaker failure scenarios.