Abstract Fischer-Tropsch waste water (FTW) is with complex organic compositions, and is toxic/stinking odor. So far, FTW is very difficult to be treated in industry. In this work, Fe-based bi-MOFs heterojunctions, i.e., MIL-88A(Fe)@MIL-88B(Fe) are synthesized through internal extended growth of rod-like MIL-88A on spindle-like MIL-88B. The compositions, structure and characteristics are systematically investigated. By virtue of larger surface area, rich active sites and strong interfacial coupling, this bi-MOFs catalyst establish better h+-e− separation/transfer. As expected, this bi-MOFs hybrid materials shows remarkable photo-catalytic performance toward FTW remediation by the help of ozone. The COD removal in bi-MOFs/O3 system is 4.2 times higher than that of ozonation alone. Furthermore, h+, O2− and OH are the predominant active radicals for FTW remediation. Bi-MOFs displays acceptable stability after 5 cycles. This work provides a new way for photo-catalytic ozonation and may drive the development of MOFs-based photo-catalytic ozonation for waste water treatment, not limited in FTW.