Two-dimensional covalent organic frameworks (COFs) are an emerging class of photocatalytic materials for solar energy conversion. In this work, we report a pair of structurally isomeric COFs with reversed imine bond directions, which leads to drastic differences in their physical properties, photophysical behaviors, and photocatalytic CO2 reduction performance after incorporating a Re(bpy)(CO)3Cl molecular catalyst through bipyridyl units on the COF backbone (Re-COF). Using the combination of ultrafast spectroscopy and theory, we attributed these differences to the polarized nature of the imine bond that imparts a preferential direction to intramolecular charge transfer (ICT) upon photoexcitation, where the bipyridyl unit acts as an electron acceptor in the forward imine case (f-COF) and as an electron donor in the reverse imine case (r-COF). These interactions ultimately lead the Re-f-COF isomer to function as an efficient CO2 reduction photocatalyst, while the Re-r-COF isomer shows minimal photocatalytic activity. These findings not only reveal the essential role linker chemistry plays in COF photophysical and photocatalytic properties but also offer a unique opportunity to design photosensitizers that can selectively direct charges.