To resolve the problems of relativity translation variant and relativity rotation variant existed in the two medical images, combining the removing characteristics and rotating characteristics in image signal Fourier transform, a method of medical image registration combining with frequency domain and time domain is put forward based on the well-known Fourier property. The method decouples the estimation of rotation and translation. It determines rotation parameters based on amplitude spectrum correlation in frequency domain and estimation translation parameters based on intensity value correlation in time domain. The experimental results of nuclear medical image registration and multi-modality medical image registration show that this method is a very robust and fast registration method with high accuracy.