The development of science and technology has brought about tremendous changes in both the virtual and real worlds. The quick response code (QR code), a kind of two-dimensional barcode, has become an important interface between the two, playing the roles of advertising, marketing, transaction payment, and information authentication. The traditional QR code only has black-and-white information dots. It is difficult to distinguish the content from the appearance and also is easy to be copied. Therefore, for the protection of information and convenient interpretation, how to enhance the security and beauty of the QR code has also been studied by researchers all over the world. Therefore, this study proposes a double-encrypted graphic QR code to modify the previous halftoning technology, to enhance its aesthetics and to perform recognition analysis. The digital halftoning technique is used to hide the second QR code in the cover QR code, and the graphic QR code of the 41 × 41 modules (the sixth version) is obtained. The fourth version QR code has 33 × 33 modules. The codeword data of the fourth version QR code is hidden around the graphic QR’s codeword, which did not affect the central area of the QR code, and its image quality was enhanced. Each module in the graphic QR code is divided into 3 × 3 sub-modules, and the explicit 41 × 41 QR code information is embedded in the middle of the 3 × 3 sub-modules. The 33 × 33 QR codeword information, according to the pseudo-random number generated by the key, is hidden in one of the other eight sub-modules, and the remaining seven sub-modules were used to display the gradation of the cover image. To study the recognition, the graphic QR code is outputted at four different sizes and then all of them are scanned for data recognition. The research results show that the modified double-encrypted QR code has better image quality, and the larger size of the QR code has better recognition rate. In addition to the double hidden information, the graphic QR code generated by this research could achieve anti-counterfeiting function and be aesthetically pleasing. In the future, double-encrypted graphic QR code could also be used to various image value-added applications that require halftone images.