The relationship of stacking density, refractive index and substrate temperature is obtained by statistical thermodynamics theory and thin film growth mechanism. Monolayer SiO2 thin films are fabricated at different substrate temperatures and deposition rates by electron beam evaporation technology. The relationships between deposition rate and surface uniformity , the refractive index are studied. The influence of substrate temperature on the refractive index, transmittance, morphology, microstructure of thin films is emphatically analyzed. It shows that the surface roughness decreases, the crystalline grain gap narrows, the refractive index and transmittance increase, absorption degree reduces with the increasing of substrate temperature. When the substrate temperature is 500 ℃, the transmittance of SiO2 thin films in the visible light is above 99.4%. Through fitting experimental data, theory calculation agrees well with the experimental results.