Covalent organic frameworks (COFs) have demonstrated significant potential as photocatalysts for efficiently generating hydrogen through photocatalytic water splitting. However, the design of COFs with distinct organic unit blocks at a molecular level profoundly influences their photocatalytic performance. In this study, we synthesized a series of β‐ketoamine COFs through molecular engineering of nitrogen sites, including phenyl‐structured TpBD, phenylpyridine‐structured TpPpy, phenylpyrimidine‐structured TpPpm, and bipyridine‐structured TpBpy. Advanced characterization techniques reveal that TpPpm and TpBpy with more nitrogen sites exhibit superior efficiencies in electron transfer and charge separation compared to TpBD and TpPpy, thereby endowing them with enhanced photocatalytic performance for hydrogen evolution from water. As a result, the photocatalytic hydrogen production rates of TpPpm (33.80 mmol g−1 h−1) and TpBpy (29.18 mmol g−1 h−1) surpass those of TpBD (20.82 mmol g−1 h−1) and TpPpy (27.49 mmol g−1 h−1). Additionally, due to the different plane symmetries between Ppm and Bpy resulting from the various positions of nitrogen sites, TpPpm displays superior photochemical properties and better photocatalytic performance compared to TpBpy. Moreover, theoretical calculation results further confirm the exceptional intramolecular charge transfer ability of TpPpm among all COFs. This work underscores the significance of precisely controlling N sites in COFs for designing high‐performance photocatalysts.