We present an ultra-small photonic crystal-based test tool for gas permeability of polymers. It features a fully-etched photonic crystal (PhC) structure occupying an area of 20 µm × 800 µm on silicon-on-insulator wafer. The light-matter interaction in the PhC cavity with deformed Polydimethylsiloxane (PDMS) under pressure difference was investigated with finite element method and finite-difference time-domain method numerically. Next, three PDMS membranes of different mixing ratios were utilized for the characterization of gas permeation flux. The feasibility and effectiveness of the proposed working mechanism are verified through clearly distinguishing the gas permeability of these three testing samples. Compared with conventional test tools, this proposed test tool has fast response while it consumes less testing gas volume in a testing system with reduced footprint. Potentially, it can be integrated into lab-on-a-chip devices to measure gas permeation in nano scale.