The selective removal of Fe particles from carbonized Fe-MOFs presents an intriguing strategy for developing efficient peroxydisulfate (PDS) activators. It is commonly accepted that their outstanding performance is largely attributed to the high specific surface area/pore volume. However, our investigation into the structure–function relationship of these materials has revealed new insights. In this study, a highly dispersed single-atom Fe and Fe3O4 clusters anchored hierarchical-pore carbon (CM88-H) was obtained via post-acid treatment of carbonized MIL-88B (CM88). Various characterizations were comparatively conducted to highlight the beneficial effects of iron dissolution. The CM88-H/PDS system achieved a notable BPA degradation efficiency, with a reaction rate of 0.323 min−1, which is 3.94 times higher than that of the CM88/PDS system. DFT calculations indicate that the Fe3O4 clusters optimize the charge distribution around single-atom Fe, promoting favorable PDS adsorption and facilitating a higher oxidation state of CM88-H. As a result, BPA can be completely degraded within 10 min with 0.1 g/L CM88-H and 0.05 g/L PDS via both radical and non-radical pathways. The CM88-H/PDS/BPA system performs effectively under various conditions, with a general reduction in toxicity. Furthermore, the CM88-H/PDS system shows broad oxidation activity towards BPA substitutes and pollutants with high ionization potential (IP). Notably, the CM88-H sponge-based fixed-bed catalytic reactor demonstrated satisfactory BPA degradation, highlighting the promising application of CM88-H in water purification. This study provides a sustainable solution for water treatment and accelerates the practical application of powdered nanocatalysts to improve water quality.