Silicone rubber has an important application as a thermal interface material for its advantages in insulation, heat resistance, etc. The thermal conductivities at different crosslinking densities are calculated by non-equilibrium molecular dynamics. The results show that the thermal conductivity increases with crosslinking density increasing. The thermal conductivity can increase by 40% when the crosslinking density is 80%, which is because the spatial network structure formed by crosslinking shortens the length of heat transfer along the atomic chain, which makes the thermal conductivity increase greatly. The position of crosslinking bond has little effect on the thermal conductivity under the same crosslinking density, i.e. there is no significant difference in the thermal conductivity of the cross-linked structure between the end-cross-linking position and the middle-cross-linking position. However, the increase of the interval between the crosslinking points is beneficial to the increase of the thermal conductivity. The phonon densities of state under different crosslinking densities are calculated, and the heat conduction mechanism of crosslinking structure is analyzed.