Layered structures accommodate guest molecules and ions in the inter-layer space through intercalation. Organic layered compounds, such as layered polymers, have both intercalation and dynamic properties. Here intercalation-induced tunable temperature-and mechanical-stress-responsive color-change properties of crystalline layered polydiacetylene (PDA) as an organic layered compound are reported. In general, organic materials with stimuli responsivity are developed by molecular design and synthesis. In the present work, intercalation of guest metal cations in the layered PDA directs tuning of the stimuli-responsive color-change properties, such as color, responsivity, and reversibility. Whereas PDA without intercalation of metal ions distinctly changes the color from blue to red at the threshold temperature, the PDA with intercalation of the divalent metal ions (PDA-M2+) shows a variety of color-change properties. The present study indicates that intercalation has versatile potentials for functionalization of organic layered compounds.