In order to reduce operational risks and to improve the risk management and control level in substation, a substation operation safety monitoring and management system (3D2S2M) has been structured based on three-dimensional (3D) laser modeling technology. In this paper, we introduce how to build such a system and to describe its implementation details. A 3D lidar scanning technology is used to perform a holographic scan of the whole internal area in a substation to obtain color point cloud data of buildings and all equipment. Then, a novel 3D visualization safety monitoring and management system, named 3D2S2M, is developed by performing a 3D reconstruction of the point cloud data. Based on the real 3D scene model of 3D2S2M, the method of 3D distance measurement is used to replace manual on-site investigation for improving operation and maintenance efficiency. In addition, a real-time high-accuracy localization method is proposed, in order to identify and analyze the positioning and the behavior of the personnel, and the movement trajectory of the equipment. By combining positioning information and the electronic fence that used in 3D2S2M, risk levels of the personnel (or equipment) are evaluated and the corresponding alarm is issued to prevent dangerous behavior, thereby the operation risk is reduced in substation.