KOMPSAT-2 like other high-resolution satellites has the time and angle difference in the acquisition of the panchromatic (PAN) and multispectral (MS) images because the imaging systems have the offset of the charge coupled device combination in the focal plane. Due to the differences, high altitude and moving objects, such as clouds, have a different position between the PAN and MS images. Therefore, a mis-registration between the PAN and MS images occurs when a registration algorithm extracted matching points from these cloud objects. To overcome this problem, we proposed a new registration method. The main idea is to discard the matching points extracted from cloud boundaries by using an automatic thresholding technique and a classification technique on a distance disparity map of the matching points. The experimental result demonstrates the accuracy of the proposed method at ground region around cloud objects is higher than a general method which does not consider cloud objects. To evaluate the proposed method, we use KOMPSAT-2 cloudy images.