Two-dimensional silica nanoparticle assemblies were obtained by deposition of bubble made from a surfactant solution containing nanoparticles onto hydrophobic silicon substrate. The morphologies of the nanoparticle assemblies can be finely controlled by several experimental parameters, including surfactant concentration, nanoparticle concentration, and deposition time. Monolayer of nanoparticles with surface coverage of about 100% can be obtained under appropriate conditions. The method can also be applied to another hydrophobic substrate, HMDS (hexamethyldisilazane)-modified silicon substrate. Furthermore, it can be applied directly to lithography patterned substrates, meaning a high compatibility with the well-developed conventional top-down approaches to nanodevices. This bubble deposition technique is expected to be a promising method in the field of nano-object assembly and organization and has great application potentials.