The invention discloses a preparation method of an epoxy functional core-shell structure magnetic polymer microsphere. The core of the core-shell structure magnetic polymer microsphere disclosed by the invention is ferroferric oxide nanometer crystal druse; the shell layer of the core-shell structure magnetic polymer microsphere is cross-linked polymer containing epoxy functional group. The preparation method comprises the following three steps of: (1), preparing the ferroferric oxide nanometer crystal druse with a high value of saturated magnetic by adopting a solvothermal method; (2), modifying the surface of the ferroferric oxide nanometer crystal druse into a dual-bond functional group by adopting a sol-gel method; (3), coating the polymer shell layer with the epoxy functional group on the surface of the ferroferric oxide nanometer crystal druse by adopting a distillation-precipitation polymerization method to obtain the epoxy functional core-shell structure magnetic polymer microsphere. The epoxy functional core-shell structure magnetic polymer microsphere is narrowly distributed in grain size, controllable in magnetic content, high in surface epoxy radial reaction activity, easy to modify the functional groups including ammonia group, hydroxyl, group, the mercapto group and the like on the surface, capable of being applied to the industrial waste water treatment field by efficiently adsorbing a plurality of heavy meals or organic pollutants, and good in application prospect.