Improving carrier transport rate and suppressing carrier recombination are two huge challenges in the photocatalytic applications of covalent organic frameworks (COFs)-based semiconductors. In this study, we propose a strategy to enhance carrier transport efficiency by regulating the local microenvironment of the electronic characteristics in the acceptors through structural modification. Three different functional group-modified fluorenone-based COFs were successfully synthesized through precise design. The results demonstrate that the photocatalytic hydrogen evolution activities of COFs modified with electron-donating functional groups are significantly higher than that of COFs modified by electron-withdrawing functional groups. Specifically, the photocatalytic hydrogen evolution performance of phenyl-modified FOOPh-COF could reach 228.5 mmol h−1g−1, which is 11.8 times higher than that of Br atom-modified FOOBr-COF (19.3 mmol h−1g−1). Femtosecond time-resolved transient absorption spectroscopy (fs-TAS) results reveal that introducing phenyl groups into the acceptor significantly enhances its inhibitory effect on the carrier recombination. Density functional theory calculations further prove that modifying the acceptor by electron-donating functional groups can achieve the increased electron density in the CO active center. The electrons in the CO region in the phenyl-modified fluorenone structure are more enriched and delocalized, which can enhance the speed of electron migration, shorten the migration distance, and inhibit carrier recombination. After loading Pt, it has the lowest H* adsorption-free energy among three samples. This work clarifies the importance of the functionalization modification of COFs’ acceptors in regulating the local electronic environment and further provides new insights into the structure–activity relationship of fluorenone-based COF-based photocatalysts.