This study aimed to develop a three-dimensional motion analysis for a natural knee joint, with high precision in vivo using an image matching technique with high-resolution X-ray image from flat panel detector (FPD). The image matching was performed determining the strength of a correlation between X-ray images and computer simulating images. However, the number of pixels in a whole reconstructed image was so huge. Therefore, in this study, several windows were set up, in which a region of interest was determined to calculate instead of viewing the whole region of the image. Computer simulating image was created by the three-dimensional solid model. Three-dimensional solid models were reconstructed using computed tomography (CT) data. We report the results of a motion pattern in analysis for a natural knee joint during deep flexion using the method.