We report a simple and effective method to generate hydrophilicity-contrasted patterns on porous thin films containing nanometer sized pores. The porous thin films were prepared by removal of the organic polymer phase, denoted as porogen, from the nanohybrid of poly (methylsilsesquioxane) (PMSSQ) and the porogen where nanoscopic porogen domains are phase separated and entrapped in cross-linked PMSSQ matrix. Selective masking the UV radiation during UV/ozone treatment produces patterns of contrasted hydrophilicity. Hydrophilic patterns with resolution of ∼4 μm surrounded by hydrophobic regions were obtained by this patterning process. The nanoporous structure of patterns provides higher number density of reaction site, which was proved by the enhanced intensity of a fluorescent dye attached on patterns.