The interface widely exists in composite material, and it plays a decisive impact on the thermal properties of mesoporous composite material. Study on the thermal conductivity of the interface is very important to know and understand the heat transfer mechanism of mesoporous composite material. In this paper, the simulation method of non-equilibrium molecular dynamics was used to calculate the interfacial thermal resistance between base material and filler in the mesoporous composite material, and the interfacial thermal resistance was analyzed with different temperature and different quality of material. Furthermore, the interfacial thermal resistance was used to modify the effective thermal conductivity of the mesoporous composite material. The results showed that the magnitude of the interfacial thermal resistance was 10-11m2·K·W-1 and it would gradually decrease with the temperature increasing. Since temperature increasing leads to the phonons' number increasing at the interface, the number and the energy of phonons penetrating the interface will increase. The greater the difference of the interface material quality, the higher the interfacial thermal resistance. The effective thermal conductivity of the mesoporous composite material can be decreased by downsizing the pore diameter, reducing the length of nanowires, increasing the distance between the nanowires or reducing the filling rate of the nanowires.It can be seen that, with the increasing of the pore size, the effective thermal conductivity of the mesoporous composite of the Z direction decreases, and those of X direction and Y direction have no obvious change. The effective thermal conductivity considering the interfacial thermal resistance is smaller than that without consideration, so it will be known that the interfacial thermal resistance can reduce the thermal conductivity, especially under the small pore diameter. The percentage of the interfacial thermal resistance is between 1%-7%, which will drop off gradually with the increasing of pore size. The effect of reducing the thermal conductivity through the interfacial thermal resistance will be more significant by decreasing the pore diameter and the distance between the nanowires, or increasing the length of nanowires and the filling rate.