The invention belongs to the field of resource utilization and chemical separation, and relates to a preparation method of phenylboronic acid modified magnetic chitosan, which comprises the followingsteps: preparing a nano Fe3O4 solid by using a solvothermal method, dispersing the nano Fe3O4 solid in water, mixing a formed mixture with an acetic acid solution of chitosan, and conducting reactingto obtain a Fe3O4@chitosan solid; mixing the Fe3O4 / chitosan solid with epoxy chloropropane in an alkaline solution, and conducting washing with water to neutrality for later use; dispersing the Fe3O4@chitosan in a NaOH solution for alkalization for 12-48 hours, adding a succinic anhydride-containing DMF solution, and carrying out a water bath reaction to obtain a carboxylated Fe3O4@chitosan solid;and finally, fully mixing the carboxylated Fe3O4@chitosan solid with EDC and NHS, and adding 3-aminophenylboronic acid to react for 6-18 hours, thereby obtaining the product. According to the method,boric acid is replaced by surface modification, so that the shikimic acid with a cis-dihydroxy structure is enriched on the surface of the material, the shikimic acid is separated and recycled by magnetic separation, and the purity and yield of the shikimic acid are effectively improved. The method has a good application prospect in the field of enrichment, separation and purification of naturalproducts with cis-dihydroxy structures, and has the advantages of energy conservation, environmental protection, convenience in recovery and the like.