Defects, such as crystal vacancy and impurity oxygen, introduced during preparing processes of the ceramic seriously damage the thermal conductivity of silicon nitride. To explore the effect of defects on the material, various silicon nitride models with different defect states were designed and studied by molecular dynamics simulation method with considering the ratio, distribution, and position of defects, as well as the temperature. Simulation results show that the thermal conductivity of silicon nitride decreases with the increase of defects and the temperature. Typically, the thermal conductivity of silicon nitride decreases obviously in cases those defects are concentrated into a block that lies across the flux pathway in the material. The position of the defects present in the crystal lattice of silicon nitride also shows a significant effect on the thermal conductivity. Such variation of defect ratio and temperature on thermal conductivity is verified by calculating the phonon density of states of the silicon nitride models. The research results provide important guidance for the preparation of silicon nitride ceramics with high thermal conductivity.