In chemical membrane cleaning, the challenge is to efficiently remove irreversible fouling while minimizing the impact on membrane materials. Particularly, traditional hypochlorite cleaning will further lead to the generation of toxic halogenated by-products. To address these issues, a combined system composed of peroxymonosulfate and chloride (PMS/Cl−) was applied to clean irreversible-humic-acid-fouled polyethersulfone (PES) membranes. After fouled membranes were soaked for 1 h in a PMS/Cl− solution (10 mM/15 mM) at 25 °C under neutral conditions, 94% flux recovery and 96% resistance removal were realized. Surface properties of virgin and cleaned membranes were very similar, confirming the effectiveness of the PMS/Cl− solution in removing irreversible foulants. The stability of membrane separation performance during multiple fouling and cleaning cycles further confirmed the minimal impact on membrane materials. Rapid diminution of the peaks centered in the region of fulvic-like and humic-like components, monitored under 3D-fluorescence for the cleaning solution, was attributed to PMS-catalyzed chlorination, thereby revealing the primary foulant detachment mechanism. Crucially, the approach exhibited lower toxicity than hypochlorite, as evidenced by reduced halogenated by-products and lower acute toxicity to Photobacterium phosphoreum T3. Overall, this novel cleaning system is promising for the efficient and environmentally friendly removal of irreversible organic foulants in practical water-treatment.