The defects of common drug anti-counterfeit systems were analyzed and the basic principles of the PDF417 barcode were introduced. The invisible method of PDF417 by IR invisible ink printing and the encryption method of treble barcodes based on DES, ECC and RSA were discussed. A drug anti-counterfeit system based on invisibly encrypted PDF417 barcode was designed. The working principles, structure design, and software design of the anti-coun-terfeit system was illustrated in details. The anti-counterfeit capability of the system was analyzed. The result indicated that this system is powerful enough in anti-counterfeit and proper for the anti-counterfeit of drugs. Besides, it can effectively put an end to the spread of counterfeit drugs and fully protect the rights and interests of sellers and consumers.