The invention provides a freight transport motor train intelligent loading system. The system comprises containers provided with RFID chips, a rectilinear transport system which is arranged in a carriage in the longitudinal direction of the carriage of a freight transport motor train and can convey the containers in the longitudinal direction of the carriage on the two sides of the rectilinear transport system, two end rotation systems which are arranged at the two ends of the rectilinear transport system and can rotationally convey the containers from one side of the rectilinear transport system to the other side, door region connecting systems which are arranged in the positions of door regions of the carriage and can connect the containers to the outside of the carriage or connect the containers outside the carriage to the inside of the carriage, and a motion control system interactively communicating with the RFID chips and electrically connected with the rectilinear transport system, the end rotation systems and the door region connecting systems. Rectilinear, rotating and connecting motion of the containers and accurate location of the containers can be automatically controlled in the narrow space in the carriage.