Phase transition is a promising aspect of DNA as biopolymers. Anionic DNA oligonucleotides easily form complexes with cationic polypeptides such as polylysine, and duplex formation significantly influences their complexation and resulting microcompartments. In this study, phase transition of microcompartments containing DNA and polylysine was systematically induced by modulating duplex formation of arylazopyrazole-conjugated oligonucleotides with light. We demonstrated that UV irradiation destabilized DNA duplex and generated isotropic coacervates, while duplex stabilization by visible light irradiation caused the formation of liquid crystalline coacervates. This photocontrol of phase transition was highly repeatable, and similar changes were observed even after ten cycles of light irradiation. Our approach would provide a robust control layer to the development of tailor-made microcompartments.