Atomic‐level modulation of covalent organic frameworks (COFs) structure for enhanced photocatalytic oxidation is highly important but still challenging. Herein, a series of β‐ketoenamine‐linked COFs have been synthesized by using 2,4,6‐triformyl‐phloroglucinol (Tp) as a modular molecule, 5,5′‐Diamino‐2,2′‐bipyridine (Bpy), and 3,6‐Pyridazinediamine (Dz) linkers with atomic level N sites substitute 4,4′‐diamino‐bipheny (BD) and 1,4‐phenylenediamine (Pa) to construct COFs with adjustable photocatalytic performance. Mechanism study reveals that in COFs with N sites‐based linkers, 1O2 adsorbed on the pore walls of TpBpy‐COF (−4.23 kcal mol−1) and TpDz‐COF (−4.63 kcal mol−1) with higher adsorption energy than on TpBD‐COF (−2.73 kcal mol−1) and TpPa‐COF (−2.17 kcal mol−1), enabling 1O2 activation and high catalytic performance toward thioether oxidation with almost >99% conversion, outperforming most reported organic photocatalysts. Notably, TpBpy‐COF exhibits a superior catalytic activity for thioether oxidation (e.g., aromatic thioethers, aliphatic sulfide, and Mustard Gas sulfide) because of its narrow bandgap, fast charge separation and transfer ability, and single‐ended activation ability. This study provides a novel and effective strategy for modulating exciton effects and photocatalytic activity of COFs‐based organic photocatalysts at the atomic level.