In this study, the low-crystalline bimetallic metal-organic frameworks (MOFs) of L-MIL-53(Fe, Mn) and L-MIL-53(Fe, Cu) (MIL: Material of Institute Lavoisier) were successfully developed as photo-Fenton catalysts, exhibiting significantly enhanced degradation performance (15.2 and 2.49 times increase in reaction rate constant, respectively) for ciprofloxacin (CIP) in contrast to their crystalline counterparts. That were mainly attributed to the intensified synergism between hetero-metal nodes. Specifically, taking L-MIL-53(Fe, Mn) as an example, the formed electron-rich Fe sites along with the strengthened roles of Mn for enlarged specific surface area, enhanced visible-light absorption and separation and transportation of photo-induced carriers in the low-crystalline state, are responsible for acceleration of Fe(II)/Fe(III) and Mn(II)/Mn(III) cycles, beneficial for H2O2 activation. Moreover, increased metal coordinately unsaturated sites (CUSs) are favorable for more H2O2 coordination. This work gives a deep insight into the heterogeneous photo-Fenton mechanism of the bimetallic MOFs in their low-crystalline state.