Plasma enhanced chemical vapor deposition (PECVD) method is applied to prepare SiO2 thin films, and the compactness is characterized by refractive index. The relationship between SiO2 thin film compactness and radio-frequency (RF) power, substrate temperature, chamber pressure, N2O/SiH4 flow rate is studied. Refractive index is measured by Filmetrics thin film thickness gauge F20 and surface microstructure is measured by focus ion beam scanning electron microscopes (FIB-SEM). Energy dispersive X-ray (EDX) is used to analyze the influence of Si, O and N element contents in thin films on the compactness with different process parameters. Design of experiments (DOE) of multi-factors is carried out. The optimum refractive index and structure growth condition under various conditions are got. The mechanism of compactness of SiO2 thin film changing with process conditions is studied.