To optimize the heat dissipation performance of microelectronic equipment, optical instrument, and optoelectronic devices, it’s necessary to explore the heat transfer mechanism of the nanostructure in them, however, due to the limitation of the research objects, there isn’t a uniform simulation method for the thermo-physical properties of such nanostructure. Therefore, this paper aims to study the thermo-physical properties of nanostructure in microelectronic equipment. At first, by structuring Si super lattice nanowires in a specific direction and then using the Ge atoms to replace the Si atoms in the nanowires, this paper built a model for the periodic Si/Ge super lattice nanowires. Then, this paper performed integral operation on the dynamic equations of the two types of atoms using the time integration algorithm to attain the trajectories of Si and Ge atoms in the nanowire structure of the microelectronic equipment, and discussed the influence of the size and geometrical shape of the cross section of nanowires on thermal conductivity. After that, this paper simulated the structure of the nano-scale SiC material, selected appropriate cut-off radius, and optimized the structure of the nanostructure model based on the Discover Minimization module. At last, the thermal conductivity of the nanostructure was calculated and its thermo-physical properties were analyzed.