Wettability control of porous materials is significant in lateral flow immunoassay, microfluidic systems, microdroplet manipulation, and so on. In this report, formation of metal oxide layers on self-organized polymer honeycomb films to control surface wettability by simple sol-gel coating and UV-O3 treatment was demonstrated. By the combination of bottom-up and top-down processes, silica thin layers can be formed by retaining their original three-dimensional honeycomb structures. Furthermore, photopatterning of metal oxides on honeycomb films can be achieved by UV irradiation through photomasks. Site-selective wettability control of honeycomb films was realized by patterning silica layers on the surface of the film.