It is the first time that domestic civil large aircraft has been developed, which lacks the technical experience of airborne system-level airworthiness qualification, and the research of radiation emission at home and abroad is mainly based on simulation evaluation, while the simulation results are used only as a reference in the airworthiness qualification process and cannot be used as evidence of conformity. And there is little airworthiness test experience on complex system-level. In this paper, taking civil aircraft flight control electronic system as an example, translate airworthiness compliance requirements into engineering requirements, analyze the complexity characteristics of civil aircraft flight control system, build flight control electronic system level radiation emission test system, and improve the system level airworthiness qualification test and optimization process, providing experience for the airworthiness qualification of civil aircraft complex system. The results show that the radiation emission of flight control electronic system is greatly affected by the system environment, and it is necessary to consider the influence of test setup layout and show the system compliance to the RTCA/DO-160G requirements.