Polydiacetylene (PDA) have been used to detect various toxic chemicals using their unique blue-to-red color transition properties. However, uncontrolled light and unexpected “clutter” can restrict the remote detection of colorimetric signals of PDA sensors at a significant distance from optical readers. Here, we created a self-referenced nerve agent vapors remote sensing system using oxime functionalized PDA embedded porous silicon photonic crystals. Photonic crystals have two stop bands, one overlapping the red phase PDA absorbance spectrum and the other as a reference being neither the blue nor red phase region of the PDA spectrum. The intensity ratio of the two stop bands showed a colorimetric change of PDA in the spectrum of reflected white light. This ratio was maintained regardless of brightness and was reduced only through reaction with organophosphate of nerve agent simulant. The approach can be applied to build a new PDA-based remote detection system.