Zinc oxide (ZnO), as a conventional semiconductor material, has excellent characteristics, such as piezoelectricity, photoelectricity, gas sensitivity, etc. With the improvement of nanopreparation technology, different types of nanostructrued ZnO compounds have appeared and their heat conductions have become a main research topic in nanodevices. In order to study the effects of grain boundary on the thermal properties of materials of this kind, bicrystal ZnO containing small-angle and high-angle grain boundaries are constructed by the embedded dislocation line and coincidence site lattice method. The variation of grain boundary energy with tilt angle is studied by the non-equilibrium molecular dynamics simulation. In addition, the dislocation density is calculated by using the Frank-Bilby formula. Our results show that the grain boundary energy and dislocation density increase with the increase of tilt angle in a small-angle region, and they tend to be stable in a high-angle region. The tilt angle of 36.86° is defined as the transition angle. The trend of the Kapitza resistance is the same as that of the grain boundary energy and satisfies the theoretical value from the extended Read-Shockley model. Furthermore, it is found that both the Kapitza resistance and thermal conductivity have a significant size effect. When the sample length is between 23.2 nm and 92.6 nm, the Kapitza resistance decreases sharply with the increase of the length and then tends to be stable. The thermal conductivity of the sample increases with length increasing, but is always less than that of the single crystal. At the same time, temperature is an important factor affecting the heat transport properties. The Kapitza resistance and thermal conductivity decrease with temperature increasing. At different temperatures, the Kapitza resistance of 38.94° grain boundary sample is greater than that of 5.45° grain boundary sample. In order to further explore the influence mechanism of grain boundary angle on heat conduction, the phonon state density of 5.45° and 38.94° grain boundary sample are calculated. The results indicate that the high-angle grain boundary has stronger scattering for acoustic branch phonons and the peak frequency becomes lower, whereas the optical branch ones have almost no effect on the heat conduction.