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Nanocrystalline ZnO is widely used in the field of microelectronics, and its thermal conductivity has an important effect on the performance of electronic devices. In order to explore the effect of grain boundary geometry on the thermal conduction of nanocrystalline ZnO,,the grain boundary geometries were abstracted into several typical structures. On this basis, the calculation of grain boundary surface roughness and the effect of phonons incident angle on specular reflectance were discussed, and the calculation model of grain boundary specular reflectance was improved. PhonTS software was used to solve the boltzmann transport equation iteratively to obtain the perfect lattice thermal conductivity of nanocrystalline ZnO. The thermal conductivity of nanocrystal ZnO was calculated based on the molecular dynamics theory, and effects of specular reflectance, phonon incidence angle and grain size on the thermal conductivity were analyzed. The results showed that: (1) the decreases of grain boundary surface roughness or the increases of phonon incidence angle will increase the specular reflectance of grain boundary; (2) phonons specular reflectance at grain boundary will not generate thermal resistance, and the thermal conductivity of nanocrystalline materials increases with the increase of specular reflectance; (3) the thermal conductivity of nanocrystalline ZnO shows a strong size effect, which decreases with the increasing of grain size.