There are shortcomings of binocular endoscope three-dimensional (3D) reconstruction in the conventional algorithm, such as low accuracy, small field of view, and loss of scale information. To address these problems, aiming at the specific scenes of stomach organs, a method of 3D endoscopic image stitching based on feature points is proposed. The left and right images are acquired by moving the endoscope and converting them into point clouds by binocular matching. They are then preprocessed to compensate for the errors caused by the scene characteristics such as uneven illumination and weak texture. The camera pose changes are estimated by detecting and matching the feature points of adjacent left images. Finally, based on the calculated transformation matrix, point cloud registration is carried out by the iterative closest point (ICP) algorithm, and the 3D dense reconstruction of the whole gastric organ is realized. The results show that the root mean square error is 2.07 mm, and the endoscopic field of view is expanded by 2.20 times, increasing the observation range. Compared with the conventional methods, it does not only preserve the organ scale information but also makes the scene much denser, which is convenient for doctors to measure the target areas, such as lesions, in 3D. These improvements will help improve the accuracy and efficiency of diagnosis.