The invention discloses a preparation method of surface molecularly imprinted polymers in water phase application. The preparation method comprises the following steps: polymerizing solutions containing MOGs, glycidyl methacrylate, ethylene glycol dimethacrylate and an initiator, and subsequently conducting washing and drying to obtain a macroporous carrier; reacting the macroporous carrier with a photoinitiator, and conducting washing and drying to obtain the macroporous carrier with the photoinitiator on the surface; pre-assembling template molecules and functional monomers, then mixing the pre-assembled template molecules and functional monomers with a crosslinker and the treated macroporous carrier, conducting photopolymerization and washing, removing the template molecules, and conducting drying to obtain the surface molecularly imprinted polymer material, wherein the molar ratio of the functional monomers to the crosslinker is 1:(20-30). According to the preparation method, the macroporous material prepared by using the MOGs as a pore-foaming agent is used as the carrier and synergistically matched with the crosslinker with a high addition proportion, thereby preparing the surface molecularly imprinted polymers SMIPs with good template molecule identifying selectivity, large adsorption capacity and high adsorption and desorption speed.