Perylene bisimides (PBIs) have attracted considerable attention as functional materials due to their outstanding optical properties, thermal robustness, and strong electron affinity, with the latter arising from the low-lying lowest unoccupied molecular orbital (LUMO) energy. The introduction of bay substitution, in which the electron donation is altered through structural conversion in response to the surrounding chemical conditions, should confer stimuli-responsible optical properties onto PBIs. Squaric acid, 3,4-dihydroxycyclobut-1-ene-1,2-dione, is a type of oxocarbonic acid that shows quite high acidity originating from the resonance stabilization of its dianion form, which shows a 2π-electron system according to Hückel’s rule. The monocondensation product of squaric acid shows not only higher acidity compared to highly acidic functional groups such as sulfonic acid, but also an aromatic character. The events involving protonation and deprotonation directly impact the orbital energy level and electronic structure of the cyclobutenedione moiety, resulting in perturbation of the photo- and electrochemical properties of the substituent on cyclobutene ring. Herein we report novel PBIs bearing 3-hydroxycyclobutenedione moieties at the bay position that exhibit halochromic effects mediated by deprotonation in the bay substitutions. This property could be exploited to sense solvent polarity, pH and humidity by means of pronounced changes in absorption spectra and thin film color.