In order to solve the problems of disconnection between quality control and business process, insufficient quality planning and high control costs in the military aircraft final assembly stage, APQP application guide（MAFA-APQP） suitable for the military aircraft final assembly stage was proposed by improving the APQP guidance material of the IAQG, including theoretical models, core content and key elements, etc. The application effect of the military aircraft assembly APQP in process optimization and management, risk identification and control were verified on the aero-engine installation. The results show that the military aircraft assembly APQP is beneficial to predict and reduce risks, reduce process changes, improve military aircraft quality and delivery efficiency.