As the one of the key technologies and an important part in the design and operation of the new generation aircraftPrognostics and Health Management (PHM) technology has been widely concerned by numerous experts and scholars at home and abroad.In view of the unmanned and collaborative features of the future aviation equipmentan analysis is made to the operation scene of the PHM system for manned and unmanned aerial vehicle cooperative fleet by using the system engineering method.The system requirements are studied by modeling the system case diagram and system activity diagram.Thenthe top-level architecture of PHM for manned and unmanned aerial vehicle cooperative fleet is proposedwhich contains functional architecture designlogic architecture design and data transmission service.Some key technologies involved in the system design are also discussed.The research has certain significance for the design of the PHM system for manned and unmanned aerial vehicle cooperative fleet.