Accurate evaluation of the critical nodes in the system is essential work for a multiplatform avionics system (MPAS) for resource allocation and other works. However, current evaluation methods are either limited to the aircraft level or the function module level. There is a lack of research on the evaluation using the information of these two levels. In view of this situation, this paper researches the two-level iterative method of evaluating the importance of aircraft function modules. The influence matrix was constructed by using the node access probability calculated by the PageRank algorithm and the function module weight calculated based on centrality. In addition, the importance of aircraft nodes was used to carry out two-level iteration, and finally, the importance of aircraft function modules was obtained. The experimental results show that this method can comprehensively utilize the information on aircraft cooperative network and function module cooperative network, solve the key problems of two-level iterative evaluation, and meet the requirement of evaluating critical nodes in a system.