Abstract: This paper proposed an efficient method of image overlapping relationship analysis based on spatial index of KD tree fast search for disordered and large-scale asteroid images. In this study, the image data from asteroid exploration missions such as Bennu, Vesta, and Ryugu were used for experiments, and the proposed image matching pairs determination algorithm was comprehensively compared with the corresponding modules of USGS ISIS in order to evaluate its performance in terms of efficiency and accuracy. The results show that when processing more than a thousand images, the proposed method greatly improves the efficiency of acquiring image matching pairs while ensuring the correctness of image overlapping relationships and accuracy of bundle adjustment. At the same time, according to the obtained image matching pairs, images that meet the requirements of Stereo Photoclinometry can be quickly selected, effectively improving the quality of 3D reconstruction models of asteroid images.