Multiple charge separation has been successfully realized by a proton‐coupled electron transfer reaction in an organic cocrystal. Benefiting from the adjustable electronic energy level of the electron donor and acceptor through thermal‐induced proton migration, distinct optical absorption behaviors combined with color changes to blue or green are observed in these charge‐separated states. It is of interest to note that such charge‐separated states exhibit a longer lifetime of over a month as a result of the excellent coplanarity and π‐π interaction of the electron acceptors. Moreover, the enhanced absorption toward longer wavelengths endows the charge‐separated state with near‐infrared (808 nm) photothermal conversion for imaging and bacterial inhibition, whereby the conversion performance can be controlled by the degree of proton migration.