Accelerating the separation of carriers in the heterojunction plays vital role in the photoelectrocatalytic (PEC) process, yet it remains a challenging undertaking. Herein, a MOF-onMOF based dual S-scheme heterojunction (BiVO4 /NH2 -MIL-125(Ti)/NH2 -MIL-53(Fe), denoted as BVO/NM125/NM53) was rationally designed and prepared for PEC removing and detoxiffcation of organic contaminants (phenol, tetracycline hydrochloride, ciproffoxacin and norffoxacin). The S-scheme heterojunction was double confirmed by DFT calculation and XPS analysis. The charge transfer resistance of BVO/NM125/NM53 photoanode decreases to 1/11 of bare BiVO4 photoanode. Meanwhile, the photocurrent density was 3 times higher, demonstrating a marked improvement in carrier separation efficiency due to dual S-scheme heterojunction. The photoanode achieved 94.3 % removal of phenol within 60 min and maintained stable performance over 10 consecutive cycles, demonstrating good PEC efficiency and structural stability. The BVO/NM125/NM53 photoanode also showed effectiveness in removing antibiotics, with chlorophyll ffuorescence imaging confirming a significant reduction in the ecotoxicity of intermediates. For example, wheat seed germination, growth, chlorophyll and Carotenoid production were not affected, which was similar to that of deionized water. Radical trapping experiments and electron paramagnetic resonance (EPR) analysis identified ?O2 - and ?OH as the primary active species. This work demonstrates the effectiveness of developing MOF-on-MOF heterojunctions for visible-light response and enhancing charge separation in PEC.