Microcystin-LR (MC-LR), which is produced from cyanobacteria, is the common microcystin with a serious threat to aquatic life and human beings. And the efficient removal method of MC-LR is urgent needed. In this work, the MIL-100/MIL-53 (Fe) photocatalysts, which were successfully prepared by the electrostatic interaction with each other, were applied for the photocatalytic degradation of MC-LR. The structure and optical properties of the MIL-100/MIL-53 (Fe) photocatalysts were characterized by using SEM, XRD, XPS, FT-IR and UV-vis DRS. The very low dosage of the MIL-100/MIL-53 (Fe) photocatalysts achieved the degradation of MC-LR, and the optimized loading was the 50% MIL-100/MIL-53 (Fe) photocatalyst. Compared to MIL-100 (Fe) and MIL-53 (Fe), the MC-LR degradation was up to 96.5% after 3 h under visible light illumination with the 50% MIL-100/MIL-53 (Fe) photocatalyst due to the pore-effect adsorption and the effective separation of photogenerated carriers. The effect of coordinate immobilized layers between MIL-100 (Fe) and MIL-53 (Fe) contributed to the stable and efficient removal of MC-LR for the 50% MIL-100/MIL-53 (Fe) photocatalyst. The MC-LR photocatalytic mechanism and degradation pathway, which the photogenerated holes (h(+)) were the main active species, were proposed by radical capture experiments and LC-MS analysis.