The invention discloses a multimodal transport interworking control system. The system comprises a track system, a freight motor car, a track system controller, a freight motor car controller and a processor, wherein the freight motor car is movably arranged on a track beam of the track system, the freight motor car comprises walking wheels, an integrated lifting sling, walking driving devices connected with the corresponding walking wheels and a turning lock mechanism arranged on the integrated lifting sling, the track system controller is used for monitoring whether the track system has the operating conditions of the freight motor car or not and controlling a switch track of a suspension type turnout system, the freight motor car controller is connected with the walking driving devices and the turning lock mechanism, and the processor is connected with the freight motor car controller and the track system controller. Accordingly, by means of connection of the processor and the freight motor car controller, the turning lock mechanism and a cargo loading device are controlled by the freight motor car controller to connect or separate, the walking wheels of a freight motor car are controlled to move on the track beam, and therefore multimodal transport between a port and a railway and aviation logistics is achieved.