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This article reports the thermal conduction properties of Si/a-SiO2 heterostructure with two different interfaces weak and strong coupling strength through molecular dynamics simulation. The size and temperature dependencies on the interfacial thermal resistance of the weak coupling interface are larger than those of the strong coupling interface. The thermal conduction in Si/a-SiO2 shows strong anisotropy. The thermal conductivity, interfacial thermal resistance, and enhancement of the anisotropy can be modulated by changing the strain