Two-dimensional (2D) covalent organic frameworks (COFs) assembled using building blocks have been widely employed in photocatalysis due to their customizable optoelectronic characteristics and porous structure, which facilitate charge carrier and mass movement. Nevertheless, the development of COF photocatalysts encounters a continuous obstacle in enhancing the efficiency of photocatalysis, impeded by a limited comprehension of the orbital interaction between molecular fragments and linkers. In this study, we present a model that examines the interaction between molecular fragments in an imine-based COF at the frontier molecular orbital level, enabling us to comprehend the impact of manipulating linkers on light adsorption, exciton efficiency, and catalytic activity. Our findings demonstrate that altering the connecting orientation of 14 R-C=N-R imine linkers in 2D COFs can enhance solar-to-hydrogen (STH) efficiency under visible light from 2.76% to 4.24%. This research has the potential to provide a valuable model for refining photocatalysts with enhanced photocatalytic performance.