A robust matching algorithm based on spatial marked points is proposed to improve the reliability of threedimensional (3D) scanning registration. This methodology defines the spatial energy to describe the uniqueness of the marked points, which is based on the distance and the spatial relationship between the marked points. Besides, the uniqueness of the energy can be applied to match the marked-points and stitch them together in different views. Compared with the traditional methodology, this algorithm can significantly avoid the ambiguity problem in the process of stitching. According to the experimental results, it only takes less than 2 ms to reach the accuracy of 100% when matching the marked-points in two views, which can realize the 3D data registration of multiple-view in the real time.