Existing systems have disadvantages such as slow running speed, long time-consuming, and poor rendering effect in virtual reconstruction of architectural spatial structure. In order to solve such problems, virtual reconstruction system of building space structure is designed using laser 3D scanning technology under condition of fusion of multiple big data. The system was equipped with a 3D laser scanner and connected to computer, and the noise interference was reduced by image preprocessing module to complete the hardware design. The system improved user interface and maintenance module. Eventually, 3D model reconstruction was realized via data acquisition, data registration, coordinate transformation and 3D rendering. The results show that the system designed in this paper runs fast, and color of reconstruction results is consistent, which indicates that reconstruction results of building space structure obtained by the system are conducive to in-depth study of building space.