The growth behavior and surface topography of the deposited films formed from silane coupling agents on silicon dioxide substrate (0001) via vapor phase deposition was investigated using atomic force microscopy (AFM). The surface topography of the films adsorbed on the silicon dioxide substrates is dissimilar with different silane coupling agents and different deposition conditions: (1) the films adsorbed on the silicon dioxide substrate become smoother with the increasing temperature of the silicon dioxide substrate; (2) the surface roughness of the films increases with the increasing concentration of the silane coupling agent solutions; (3) with the increasing temperature of the carrier gas, the surface roughness of the films decreases firstly and then increases; (4) with the increasing time of deposition, the surface roughness of the films increases firstly, then decreases and subsequently increases again. In experiments, the films adsorbed on the silicon dioxide substrate was rinsed ultrasonically with toluene, the results indicate that the silane coupling agent adsorbed on the substrate by physisorption and chemisorption: the chemisorbed coupling agents present island morphology and the physisorbed coupling agents are deposited on the substrate between the islands to decrease the surface roughness of the film.