The invention discloses an electromagnetic compatible digitized model system for a whole aircraft, which comprises an aircraft parameterized surface model construction unit (1), an airborne equipment position matching unit (2), an airborne equipment interference associated unit (3), an electromagnetic environment distribution unit (4) and a sensitive equipment interference source acquisition unit(5). The invention constructs the electromagnetic compatible digitized model system for the whole aircraft by adoption of the behavioral simulation method, application of the 'grey box' theory, consideration of characteristic parameters of electronic airborne equipment from the aspect of system level, neglect of various circuit details, and digitized modeling simulation of the electronic airborneequipment of the aircraft.