Abstract: A registration algorithm based on image downsampling and phase correlation was proposed to meet the registration requirements of PCB defect detection system. First of all, in order to solve the problem that the phase-dependent sub-pixel registration method using one-sided peak has a large error at the integer displacement, a two-side peak method is proposed to judge whether it is necessary to use the two-side peak method according to the ratio of the peak-to-peak difference between the two sides to the main peak. Secondly, in order to solve the efficiency problem in the application of algorithms, the effects of different downsampling magnifications on registration speed and accuracy are discussed. The experimental results show that the maximum error and average error of the improved algorithm are smaller than that of the one-sided peak method. The 20-million-pixel image can achieve high accuracy under the condition of five times of downsampling, and the speed is improved by about 20 times. The algorithm has robustness and real-time performance.