Aiming at the characteristics of complex composition of aviation equipment system-of-systems, the fault tree analysis was introduced into the evaluation problem of aviation equipment′s structure contribution rate to system-of-systems, and an evaluation method based on fault tree analysis was proposed. The aviation equipment system-of-systems structure was constructed from the three aspects of operation equipment, information support equipment and support equipment. Furthermore, the fault tree of aviation equipment system-of-systems structure was constructed and the criticality importance index of bottom event was used to calculate the aviation equipment′s structure contribution rate to system-of-systems. And the evaluation model of aviation equipment′s structure contribution rate to system-of-systems based on criticality importance was established. Taking an aviation equipment system-of-systems as an example, the results show that the proposed method can evaluate the aviation equipment′s structure contribution rate to system-of-systems accurately and provide methodological support for short board determination and optimization of aviation equipment system-of-systems structure.