Abstract: Theoretical deduction is given to show the correctness of our approach based on the principle of integer interpolation and Fourier transform for under-sampled image. Subpixel registration algorithm and its error analysis for under-sampled image are presented. Experiment results of multi-spectral and simulated images show that our scheme has overcome the drawback of classic phase correlation, good results have been obtained for subpixel translation estimation of images of different spectral bands.