In view of the problems in traditional 3D scene simulation, such as the poor simulation effect and the inability to really feel the scene, this paper proposes the research of nano particle system scene construction based on virtual technology. By analyzing the advantages of virtual reality technology, the role of virtual reality in three-dimensional scene is determined; the method of three-dimensional geometry transformation is used to determine the scene building algorithm of virtual technology; the concept of nano particle system hierarchy is introduced to build nano particle subsystem with object-oriented concept. The functions of the system are mainly divided into system control module, user interaction module, scene management module, and nanoparticles management module. Based on the analysis of virtual technology and the construction of nano particle system, the construction of nano particle system scene based on virtual technology is realized. The experimental results show that: Based on the virtual technology, the nano particle system scene construction effect is better, and the scene construction time is less than 6 min, the work efficiency is higher, the scene is more realistic, and has a certain feasibility.