Based on the analysis and research of the airworthiness objective of integrated modular avionics system (IMA), and the characteristics of IMA system’s comprehensive and complex cross-linking with other airborne systems, the extraction strategy of IMA system’s compliance flight test subjects and the selection method of IMA system’s compliance flight test parameters are proposed. The data analysis method based on the abnormal probability matrix of the IMA system is proposed for the first time, and the abnormal state information of the IMA system can be quickly identified. The compliance flight test of the IMA system is completed with limited flight test resources, which achieves the purpose of saving flight test sorties and improving flight test efficiency. This research has been successfully applied to the airworthiness certification flight test of a certain civil transport aircraft in China, and can provide technical support for the subsequent type flight test.