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In clinical diagnosis and treatment, the images which we wanted are taken in obscuration or the object which is caught is moving during imaging, which will cause the SNR of the images to be very low, and make the image registration difficulty. To improve the quality of image quality, the joint transform correlator is used to measure the image motion between the serial images, then the images are aligned and added together to form a distinct one. The principle of this method was described firstly, to improve the accuracy of the measurement, the no-zero joint transform correlator is then put forward, and the simulation and experiment was done by using some medical images lastly. The results showed that, the joint transform correlator can measure the sub-pixel image shifts entirely even for the images with SNR = 1, and mean square deviation of the measurement error no more than 0.2 pixels, which can meet the requirement of the registration of the image absolutely.