Covalent organic frameworks (COFs) have emerged as one of the most studied photocatalysts owing to their adjustable structure and bandgaps. However, there is limited research on regulating the light-harvesting capabilities of acceptor building blocks in donor-acceptor (D-A) isomer COFs with different bond orientations. This investigation is crucial for elucidating the structure-property-performance relationship of COF photocatalysts. Herein, a series of D-A isostructural COFs are synthesized with different imine bond orientations using benzothiadiazole and its derivatives-based organic building units. Extended light absorption is achieved in COFs with acceptor groups that have strong electron-withdrawing capacities, although this resulted a decreased hydrogen generation efficiency. Photocatalytic experiments indicated that dialdehyde benzothiadiazole-based COFs, HIAM-0015, exhibit the highest hydrogen generation rate (17.99mmol g-1 h-1), which is 15 times higher than its isomer. The excellent photocatalytic performance of HIAM-0015 can be attributed to its fast charge separation and migration. This work provides insights into the rational design and synthesis of D-A COFs to achieve efficient photocatalytic activity.