Covalent Organic Frameworks (COFs) are promising in the field of photonic energy conversion. However, most efforts have been concentrated on the design of ligand geometric structures and chemical bonding relationships, while understanding the impact of stacking methods on photonic energy conversion remains a significant challenge. In this work, four COFs (1D-COF, 1D-MeCOF, 1D-tBuCOF and 2D-COF) with the same main-chain structure but different stacking methods are designed and synthesized, using photocatalytic hydrogen evolution as a model reaction. Mortise-tenon stacked 1D-MeCOF exhibits far superior photocatalytic hydrogen evolution performance to other stacking methods, and it maintains high efficiency and stability in natural seawater systems. Extensive characterization demonstrates that such a unique mortise-tenon stacking structure of 1D-MeCOF inhibits interchain slippage, enhances π-stacking, and maximizing light absorption capabilities. Furthermore, unidirectional carrier transport characteristics of one-dimensional structure can generate a strong photo-induced self-built electric field, which acts as "self-catalysis" to accelerate carrier transport. This work provides an effective design strategy and mechanistic insights on the stacking engineering of photonic energy conversion materials.