Targeting at the geometric attack problem of QR code watermarked images in the process of scanning and decoding, a new watermarking algorithm was proposed based on digital holography and Fourier-Mellin transform. Fourier-Mellin transform was used to construct geometric invariant domain, and holographic watermarking was embedded in the middle frequency of the QR code image′s DFT amplitude spectrum domain taking advantage of the strong anti-tear property of hologram. Comparative experiments showed that the algorithm proposed could effectively resist geometric distortion (rotation, scaling, clipping, and so on) of QR code watermarked images, and this algorithm was simple and had large amount of embedded information. The algorithm proposed in this paper could well balance between the robustness and the invisibility without affecting the correct identification of QR code.