In order to scientifically sort out the differences in airworthiness management of military and civilian aircraft and improve the airworthiness safety of military and civilian aircraft, the input-process-output (IPO) model in system engineering theory was innovatively applied, and airworthiness management was regarded as a management process in system engineering. A airworthiness management process IPO model based on system engineering theory was established. A differential analysis of military and civilian aircraft airworthiness management was conducted using the five elements of input, output, enable, control, and activity in the airworthiness management process IPO model. The similarity between military and civilian aircraft airworthiness management lies in the fact that both are comprehensive and full process control management aimed at ensuring the safety of aircraft engines. The differences lie in the level of management and enforcement in terms of security objectives, management institutions, standards/regulatory systems, tailorability of standards/regulations, deployment and division of labor, and regulatory methods. The specific differences between military aircraft airworthiness management and civil aircraft airworthiness management were analyzed, which provides reference opinions for the subsequent development of military and civil aircraft airworthiness management.