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An automatic multi-view point cloud merging algorithm used in structured light measurement system is presented. Firstly, an improved regional marked algorithm combined with least-squares algorithm is used to compute the center of the reference points accurately, and the 3D coordinate of the reference points is ascertained according to the theory of machine vision. Then, based on the spatial character invariability, a rapid reference points matching algorithm is proposed to acquire the corresponding relationship between the reference points with different views. Finally, the rotation matrix and translation matrix are computed by quaternion decompose algorithm to carry out the automatic multi-view point cloud merging algorithm. The result of the experiments shows great validity and practicability of the algorithm.