In integrated support engineering, the number of components in reliability block diagram is large, the level of mastering the principle of system is required to be high and the operational data is always incomplete. To resolve these problems, a method that identifies the reliability structure of system using the information of operational data and the reliability of the units was proposed. The system reliability was estimated by using the system performance information. In addition, all reliability structure models was traversed and the theoretical reliability was calculated with the system's units reliability information, then the deviations between the estimated value of system reliability and all the reliability theoretical values were calculated, and the identification results by the first N reliability structure models of the lowest deviation was outputted after sorting the deviations. The calculation results of a given example show that the combined system based on the voting reliability structure can be identified with the probability of around 80%, decreases to 3% of the scope out of all possible forms, it can significantly reduce the workload of the researcher to identify the system reliability structure.