The amorphous SiO2 and primary particle unit(PPU) of SiO2 aerogel are generated using the melting-quenching process based on the molecular dynamics method. Their thermal conductivities(TC) are also calculated by the non-equilibrium molecular dynamics(NEMD). The size effect on the TC caused by the heat source and heat sink has been taken into account. The predicted TC of the bulk amorphous SiO2 material is in good agreement with the available results in literature. Calculated results also show that the particle diameter has made the TC of the PPU show scale effect in the range of 2-6 nm though the effect is relative small. The diameter of the interface between particles has significant effect on the TC of the PPU which increase 171.61% as the interface diameter increases from 0.89 nm to 2.49 nm when the particle diameter is 3 nm. A temperature drop at the interface showed that there is interfacial thermal resistance between the neighboring particles. It is also shown that, the smaller the interface size, the bigger the interface thermal resistance.