Photoexcitation of keto-enamine allows intramolecular proton transfer from C-NH to C=O, leading to tautomerization, while the photogenerated isomers are excluded from the study of photocatalytic applications. Herein, we demonstrate the photoisomerization of keto-enamine linkages on covalent organic frameworks (COFs) induced by excited-state intramolecular proton transfer (ESIPT). Partial enolization generates partially enolized photoisomers with a mixture of keto (C=O) and enol (OH) forms, conferring extended π-conjugation with an increase in electron density. The spatially separated D-A configuration is thus rebuilt with the enol-imine-linked branch as a donor and the keto-enamine-linked branch as an acceptor, and in turn, the photoinduced charges transfer between the two adjacent branches with a long lifetime. We further prove that the partially enolized photoisomer is a key transition instead of the keto-enamine form as an excited-state model to understand the photocatalytic behaviors. Therefore, ESIPT-induced photoisomerization must be considered for rationally designing keto-enamine-linked COFs with enhanced photocatalytic activity. Also, our study points toward the importance of controlling excited-state structures for long-lived separated charges, which is of particular interest for optoelectronic applications.