To solve the problem that traditional reliability evaluation methods cannot describe the complexity of equipment system of systems (ESoS) and evaluate the mission completion probability accurately, a new-evaluation-method based on discrete event simulation is proposed. In this method, the process flow network method with expanded elements such as time and resources and activity impact factor are used to model the task flow of ESoS to clarify logical relationships between sub-tasks and activities. The discrete event simulation method is used to establish the ESoS mission completion probability simulation evaluation model, entities are generated to perform the simulation process. The mission completion probability is set the ratio of the number of entities entering the endpoint that caused the success of the mission to the total amount of all entities generated, and the simulation clock is set to record the time at which time each entity performed each activity. The mean mission time is recorded as the average time of the mission. Finally, a typical army operation ESoS is simulated as an example to illustrate the feasibility of the proposed method.