To understand and control the interfacial properties of polydiacetylenes (PDAs) vesicles with Pi-conjugated backbone is very important for their colorimetric sensing of chemical and biological targets. In this work, we adopted 10, 12-pentacosadiynoic acid (PCDA) as the model molecule to prepare PDAs vesicles in aqueous solution with different forms (from monomer to blue-to-purple-to-red phase) by controlling the UV irradiation dose. The variations of the interfacial conformation of PDAs vesicles during chromatic transitions were inspected by the adsorption behaviors of probe molecules (4-(4-diethylaminostyry)-1- methylpyridinium iodide, D289) on vesicle surface with surface-specific second harmonic generation (SHG) and zeta potential measurements. Resonant SHG signal from D289 adsorbed on vesicle surface attenuated sharply, and the adsorption free energy as well as the corresponding two-photon fluorescence signal decreased slightly in chromatic transitions. While, the change in the surface density of the adsorbed D289 molecules for PDAs vesicles with different forms was relatively small as estimated from zeta potential measurements. The attenuation of the SHG intensity was thus attributed to the overall order-disorder transition and the changed orientation of D289 molecules caused by the gradual distortion of carboxyl head group driven by backbone perturbation.