Photo-Fenton performance of Fe-based metal–organic frameworks needs to be further improved owing to little coordinatively unsaturated metal sites (Lewis acid sites) and poor photogenerated carrier separation and migration efficiency. In view of this problem, this work has developed missing-linker metal–organic framework with mix-valence coordinatively unsaturated metal site (abbreviated as CUS-Pac-MIL-100 (Fe)) for photo-Fenton degradation by thermal activation and introducing missing linker. The structure of catalysts was characterized by SEM, XRD, XPS, in-situ DRIFT, TG, BET, and EPR, which proves abundant mixed-valence coordinatively unsaturated metal sites are introduced by vacuum thermal activation and plenty of ligand vacancies are introduced by missing-linker. The conditions for TC-HCl degradation were optimized. The results indicate that CUS-Pac-MIL-100 (Fe) exhibits remarkable removal rate of TC-HCl within 80 min at 10 mL/L H₂O₂ dosage, 0.2 g/L catalyst dosage, and a wide pH range (4.0–7.0). The total organic carbon (TOC) removal rate also reaches 52.3% within 80 min. Such remarkable improvement in the photo-Fenton activity is attributed to the mix-valence coordinatively unsaturated metal sites improving the adsorption and activation ability of H₂O₂, and the ligand vacancies promoting the separation efficiency of carriers to accelerate Fe²⁺ regeneration. The catalyst also exhibits excellent cyclability and stability after multiple cycles. Further, the degradation mechanism and degradation pathways of TC-HCl in the photo-Fenton reaction has been proposed on the basis of radical quenching, electron paramagnetic resonance, and LC-MS tests. This work provides a worthy insight for the construction of high-efficiency MOF-based photo-Fenton materials.