Polymer,films with patterned microstructure have been widely applied in various industrial areas such as micro reactors, chemical sensors and micro-molded template etc. In this paper, a self-supporting polymer film with regular honeycomb microstructure is fabricated by self-organization via evaporation of polyphenylene oxide (PPO) solution in which carbon disulfide is used as solvent under humid ambience. Apart from investigation of self-organization mechanism of PPO honeycomb including nucleation, growth of water droplets condensed upon liquid supporting substrate, the quantitative relationship between honeycomb microstructure and ambient conditions is built through tremendous self-organization experiments. The controllable formation of honeycomb microstructure with desirable hydrophobicity was achieved by use of built quantitative relationship. Moreover, hydrophobicity mathematical model of self-organized honeycomb thin film was proposed, and its validation was experimentally verified.