Conjugated polydiacetylene (PDA)/silica nanocomposites with tunable mesostructures and reversible thermochromatisms were synthesized through self-directed assembly of diacetylenic silanes. In contrast to the previous studies, where the PDA side chains interacted weakly through noncovalent interactions, the side chains in the present nanocomposites are covalently connected to the inorganic silica frameworks, providing control over the molecular alignment, stability, and electronic properties. Furthermore, tuning the molecular architecture (e.g., the shape and side-chain length) allows control over the mesostructure (e.g., cubic and lamellar) and chromatic response of the nanocomposites (from irreversible to partially reversible and then to completely reversible). In addition, mesoporous PDA/silica nanocomposites have also been synthesized through co-assembly of bridged diacetylenic silsesquioxane and surfactant. Due to the covalent interactions, the nanocomposites demonstrate higher reversible chromatic transition temperatures. This work not only provides responsive robust chromatic materials toward practically reusable PDA sensors but also is of great fundamental value for the design of supramolecular assemblies and the understanding of the chromatic mechanism of PDA.