The invention relates to the technical field of automatic control. The invention discloses a bar code automatic association system. The bar code automatic association system comprises a controller, ascanner, a rejecting mechanism, a photoelectric tube, a manipulator, a PC and a reader-writer, wherein the scanner is used for scanning a bar code on a cigarette and feeding back a scanning result tothe controller; the rejecting mechanism receives a rejecting command sent by the controller to reject cigarettes which are not scanned; the photoelectric tube is used for recording the number of cigarettes and feeding back the number to the controller; the manipulator receives a grabbing command sent by the controller to grab the cigarettes; and the controller packages and sends bar code information of the cigarettes of the specified number to the PC, and the PC controls the reader-writer to write the bar code information into the RFID tag. The invention further discloses a bar code automaticassociation method of the bar code automatic association system, and the bar code automatic association method reduces the cigarette warehouse-in and warehouse-out time, saves manpower and material resources, and improves the input accuracy of cigarette carton information.