Polydiacetylenes (PDAs) has received considerable attention for their color transition from blue to red, and fluorescent emission properties. However, the reversible fluorescence studies of PDA systems have been rarely studied due to their weak fluorescence emission intensity and limitations of the experimental platform. Here, we designed a conjugated PDA organogel microstructure with various molecular interaction capabilities using maskless lithography techniques. These PDA organogel microstructures have multiple molecular interactions such as pi-pi stacking, aromatic interaction, and aliphatic interaction. Thess PDA organogel microstructure exhibit specific reversible fluorescence emission changes depending on the type of inter/intra molecular interactions during contraction and expansion when exposed to protic and aprotic solvents. Our manufacturing method of conjugated organogel microstructures using maskless lithography and the design principles of functional group that induce intra/inter molecular interaction propose a novel experimental platform to better understand the PDA’s reversible fluorescence characteristic