The pH chromism of polydiacetylenes (PDAs) is examined with respect to the molecular size and acidity of acid analytes, along with the alkyl spacer length of primary-amine-functionalized diacetylene (DA) lipids. pH turns out to be an important parameter to charge amine headgroups of PDA but a change in pH does not necessarily result in a PDA color change. The molecular size of acid analytes is identified as another factor that can produce a configurational change in PDA amine headgroups, followed by perturbation of the ene–yne conjugated backbone. In addition, the length of a flexible alkyl spacer between the amine headgroup and the amide group of the diacetylene lipids is found to strongly affect the degree of PDA chromatic transition. The longer alkyl spacer shows a smaller chromatic transition from blue to red phase. The alkyl spacer seems to provide a certain degree of freedom to the amine headgroup, thus decreasing the transfer of headgroup steric effects to the PDA backbone. These correlations found for PDA chromism are applied to the development of a system that colorimetrically detects diethyl phosphate (DEP), a degraded nerve agent simulant. PDA liposomes show a selective chromatic transition upon binding with DEP compared to other acid analytes.