The security of electronic payment has become an urgent problem. A secure Quick Response(QR) code system was proposed based on the technology of three-dimensional(3D) imaging and 3D authentication information. Firstly, the integral imaging technology was used to generate 3D digital watermark as the logo of the merchant. Secondly, identity based digital signature was carried out. Then, in the Fresnel domain, the 3D digital watermark with signature information was carried by using a secure QR code system, which was then compressed and hidden in the QR code. Finally, the users scan QR code to identify and extract the hidden data. If the signature information of verification was confirmed by users, the algorithm of reconstruction was executed, and the 3D digital watermark images were displayed. The payments were confirmed after the users were authenticated. The process of interactive authentication was completed. According to the results of experiments, the schemes can effectively prevent the 3D digital watermark from being tamper-bent, falsified, and unjustified. The proposed method not only enhances the security of scanning mobile payment, but also improves the real-time and convenience of the system. When multiple parameters of the proposed system are combined as keys, the dimensions of keys are effectively increased. The key space is broadened. The difficulty of illegal attack is enhanced, and the safety and stability of the system are improved too. It can protect the security of personal fund, and also maintain the reputation and property security of enterprises.