The non-contact three-dimensional measurement and reconstruction techniques have played a significant role in the packaging and transportation of precious cultural relics. This paper develops a structured light based three-dimensional measurement system, with a low-cost for cultural relics packaging. The structured light based system performs rapid measurements and generates 3D point cloud data, which is then denoised, registered and merged to achieve accurate 3D reconstruction for cultural relics. The multi-frequency heterodyne method and the method in this paper are compared. It is shown that the relative accuracy of the proposed low-cost system can reach a level of 1/1000. The high efficiency of the system is demonstrated through experimental results.