Harmful Microcystis blooms and microcystins have become a major hidden threat to the safety of the water environment. The application of enzymatic degradation of microcystins has been severely limited by the complex environment. In this study, chitosan-graphene (CG), prepared from green biomass, was employed as matrix material, loaded with 100–200 nm Fe3O4 nanoparticles (MCG) and immobilized microcystinase A (MlrA@MCG). The preparation of MlrA@MCG was characterized by scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, vibrating sample magnetometer and fluorescence labelling. The results of the activity analysis demonstrated that MlrA@MCG exhibited superior degradation activity for MCs, as well as enhanced heat and alkaline resistance in comparison to free MlrA. Furthermore, MlrA@MCG can be recovered simply by means of a magnetic field, and its activity remains at 48.6 % after 10 repeated uses. More importantly, MlrA@MCG and the degradation products of MC-LR were not found to be cytotoxic to human cells. It is interesting that the immobilization of MlrA resulted in a reduction in the cytotoxicity of MCG. 0.2 U of MlrA@MCG can still degrade MC-LR from 232.64 μg L−1 to 94.39 μg L−1 in water from simulated severe Microcystis blooms within 24 h, showing excellent catalytic activity and stability. The study proposed a secure and efficacious approach for the elimination of microcystins from harmful Microcystis blooms, offering a promising avenue for the improvement of environmental safety.