Functional gastrointestinal disorders (FGID) are the most common gastrointestinal disorders. The term "functional" is generally applied to disorders where there are no structural abnormalities. One of the major factors for FGID is abnormal gastrointestinal motility. We have proposed a system for assessing the function of gastric motility using a 3D endoscope. In this previous study, we established a method for estimating characteristics of contraction wave extracted from a 3D shape include contraction wave obtained from stereo endoscope. Because it is difficult to fix the tip position of the endoscope during the examination, estimation of the 3D position between the endoscope and the gastric wall is necessary for the accurate assessment. Then, we have proposed a motion compensation method using 3D scene flow. However, since mucosa has few feature points, it is difficult to obtain 3D scene flow from RGB images. So, we focused on spectral imaging that can enhance visualization of mucosal structure. Spectral image can be obtained without switching optical filters by using technique to estimate spectral reflectance by image processing. In this paper, we propose registration method of measured 3D shape in time series using estimated spectral image. The spectral image is estimated from the RGB image for each frame. 3D scene flow of feature points, that is, enhanced mucosal structure calculated by spectral images in a time series. The position change between the endoscope and gastric wall is estimated by 3D scene flow. We experimented to confirm the validity of the proposed method using papers with a grid of colors close to the background color.