Aiming at the problems of lack of design standards, high complexity and low accuracy in the design and engineering application of prognostic and health management (PHM) system for military aircraft, the design requirements of data, structure and function dimensions of PHM system are analyzed. Based on the study of the relations and characteristics of the three dimensions, the three-dimensional multiphase iterative design criteria is proposed. A three-in-one design architecture of real-time health management based on embedded system, knowledge logic visualization based on knowledge graph, and PHM system modeling based on MBSE is proposed. The PHM system design process is constructed by analyzing the PHM system design strategy, which provides a method for the engineering application of military aircraft PHM system.