The invention discloses a preparation method of surface-modified ion-imprinted polymer microspheres. The method comprises the following step: carrying out grafting reaction on a hydrophilic monomer, a first initiator, a first chain-transfer agent and ion-imprinted polymer microspheres in a first organic solvent to obtain surface-modified ion-imprinted polymer microspheres, wherein the grafting reaction temperature is 60-90 DEG C, and the grafting reaction time is 8-48 hours. The hydrophilic monomer is grafted to the surface of the ion-imprinted polymer microspheres, thereby enhancing the hydrophilicity of the surface-modified ion-imprinted polymer microspheres. The experimental result of the embodiment of the invention indicates that the contact angle of the surface-modified ion-imprinted polymer microspheres is 98.44 degrees, so the surface-modified ion-imprinted polymer microspheres are hydrophilic. Besides, the obtained surface-modified ion-imprinted polymer microspheres have excellent antijamming ability and stability.