The invention discloses an embedded health monitoring system for an active and passive structure of an aeroplane, comprising a software module, a system power supply module, a controller module, a high-speed memory module, a sensor signal acquisition module, a signal magnifying module, an acoustic emission triggering module, a channel switching module, a digital management module, an excitation signal output module, a power magnifying module and a signal transfer module. The embedded health monitoring system can monitor the health condition of the aeroplane structure on line, has the advantages of compact structure, vibration resistance, electromagnetic interference resistance, small size, light weight, convenient carrying and installation, convenience for the maintenance personnel of the aeroplane and capability of realizing onboard carrying, integrates a plurality of damage monitoring methods, and automatically extracts structural damage characteristics and distinguishes the damages. In addition, the system has good expandability so as to very conveniently collocate and expand healthy monitoring software and healthy monitoring hardware; and the system is provided with standard onboard equipment interfaces, thereby being convenient for networking of a plurality of sets of systems and communication with other onboard systems.