The invention relates to the technical field of polymer assistants, and particularly relates to a compatilizer containing an epoxy group core-shell structure and a preparation method of the compatilizer. The preparation method comprises the following steps: (1) respectively dissolving hydroxyphosphate and calcium acetate in deionized water to obtain a mixture A and a mixture B, uniformly mixing and stirring the mixture A and the mixture B to obtain a mixture C, adding a dispersing agent into the mixture C, and heating and stirring the obtained mixture to obtain a water-phase mixture; 2) addingan azo initiator and tert-dodecanethiol into a styrene monomer, and stirring the initiator and the tert-dodecanethiol until the azo initiator is completely dissolved to obtain an oil-phase mixture; and 3) slowly adding the oil-phase mixture into the water-phase mixture, heating and stirring the obtained mixture, dropwise adding a glycidyl methacrylate pre-emulsion, and heating to react, thereby obtaining the compatilizer containing epoxy groups on the surface. The epoxy group-containing compatilizer with a core-shell structure can be synthesized in a suspension polymerization manner, and thesynthesized compatilizer has good compatibility with a polymer material matrix.