Efficient charge carrier separation is widely recognized as crucial for effective photocatalytic solar energy conversion. Although certain covalent organic frameworks (COFs) exhibit visible light absorption, rapid carrier recombination often severely restricts their photocatalytic efficiency. This study presents a novel molecular‐engineering approach to enhance carrier separation in 2D substoichiometric COFs post‐treatment with polar ketone molecules. Remarkably, through molecular engineering, incorporating polar ketone molecules induces local charge polarization within the COFs, substantially improving photocatalytic hydrogen evolution performance. Specifically, the modified COFs single‐molecule junctions demonstrate a 5.6‐fold increase in efficiency compared to the unmodified COFs. Experimental and theoretical investigations provide comprehensive evidence that introducing ketone‐based single‐molecule junctions induces local charge polarization and delocalization, thereby facilitating efficient carrier separation, rapid charge transfer, and enhanced dispersion in water. These findings validate the potential of fine‐tuning the carrier separation properties of COFs at the molecular level, offering new prospects for artificial photosynthesis.