We report a new type of intercalation system using the host polydiacetylene (PDA) crystals including a carboxylic acid in the side chain in combination with various guest alkylamines. The role of the phenylene or methylene spacer between the conjugated main chain and the carboxylic acid on the intercalation property was investigated using three kinds of PDAs, i.e., poly(1,3-hexadecadiynyl-4-benzoic acid), poly(2,4-heptadecadiynoic acid), and poly(10,12-pentacosadiynoic acid), as the host polymer crystals. The color of the PDA crystals changed from blue to red by the addition of the amines. A change in the interlayer distance of the host polymer crystals according to the size of the guest amines was determined, and the inclined structure of the alkyl groups was discussed based on the powder X-ray diffraction data. We further succeeded in the direct observation of the intercalation reaction process by monitoring the color change in a large PDA crystal using optical microscopy.