Rain spots on green plum are superficial micro-defects. Defect detection based on a two-dimensional image is easily influenced by factors such as placement position and light and is prone to misjudgment and omission, which are the main problems affecting the accuracy of defect screening of green plum. In this paper, using computer vision technology, an improved structure from motion (SFM) and patch-based multi-view stereo (PMVS) algorithm based on similar graph clustering and graph matching is proposed to perform three-dimensional sparse and dense reconstruction of green plums. The results show that, compared with the traditional algorithm, the running time of this algorithm is lower, at only 26.55 s, and the mean values of camera optical center error and pose error are 0.019 and 0.631, respectively. This method obtains a higher reconstruction accuracy to meet the subsequent plum micro-defect detection requirements. Aiming at the dense point cloud model of green plums, through point cloud preprocessing, the improved adaptive segmentation algorithm based on the Lab color space realizes the effective segmentation of the point cloud of green plum micro-defects. The experimental results show that the average running time of the improved adaptive segmentation algorithm is 2.56 s, showing a faster segmentation speed and better effect than the traditional K-means and K-means++ algorithms. After clustering the micro-defect point cloud, the micro-defect information of green plums was extracted on the basis of random sample consensus (RANSAC) plane fitting, which provides a theoretical model for further improving the accuracy of sorting the appearance quality of green plums.