The work aims to put forward a frequency domain digital watermarking algorithm for QR code carrier image which has strong robustness, in order to overcome the problem that QR code image is hard to hide watermarks. Fourier holography technology subject to double random phase modulation was used to encrypt watermark and the pretreatment was made including Gaussian blur and the removal of visual sensitive area for QR code carrier image at the same time. Then the singular value matrix of holography encrypted watermark was weighted and embedded into the middle frequency coefficient of QR code after secondary wavelet decomposition and then was restored. The straight line at the edge of QR code image in the same direction was detected by Hough transform through coordinate system transformation and then skew correction was done to extract the watermark. Watermark kept good invisibility (PSNR=32.3) under the suitable embedding strength. After a series of attacks, including binarization attack, signal processing (filtering, noise and compression), geometric transformation (translation, rotation and scaling) and print-scan attack, the extracted watermark was still clearly visible. The proposed algorithm has strong robustness for various types of attacks and it can resist rotation attack at any angle, and it also meets the requirement of invisibleness. The algorithm has certain application value in QR code anti-counterfeit technology.