Atomic force microscopy ( AFM) is used for the morphology study of polyvinyl alcohol/ silica (PVA/SiO2) nanocomposites prepared by incorporating solution compounding and self-assembly technique. The results show that the strong particle-particle interaction of SiO2 nanoparticles is greatly suppressed, and the SiO2 nanoparticles are homogenously distributed in PVA matrix as spheric nano-clusters. The average size of the SiO2 nano-clusters is below 50 nm at low SiO2 loadings (<= 5 wt%). At higher SiO2 contents, the particle aggregations can be clearly observed, and the average size of SiO2 aggregates significantly reach up to 110 nm and 250 nm at SiO2 content of 10 wt% and 15 wt%, respectively. AFM height profiles demonstrate that the surface heterogeneity of the nanocomposite is governed by the SiO2 contents. The surface roughness evaluated as root mean square (RSM) of peak-to-valley height values shows that the surface becomes rougher as the SiO2 content increases, particularly, a remarkable increase in surface roughness is found at the SiO2 content of 10 wt%.