The invention discloses a preparation method of a phenethyl alcohol glycoside molecular imprinting polymer. The preparation method comprises the following steps that 1, phenethyl alcohol glycoside template molecules and a functional monomer are added into a solvent in a molar ratio of (1:8)-(1:30), prepolymerization is conducted after mixing, and prepolymerization reaction liquid is obtained; 2, after the prepolymerization reaction liquid obtained in the step 1 is mixed with a cross-linking agent and an initiator to remove oxygen, temperature is raised to conduct polymerization, and a polymeris obtained, wherein the molar ratio of the functional monomer in the step 1 to the cross-linking agent is 1:3; 3, the polymer obtained in the step 2 is ground and screened, the particles with the size of 45-100 micrometers are collected and eluted with an eluant, and then the phenethyl alcohol glycoside molecular imprinting polymer is obtained. The invention further provides the polymer preparedby using the preparation method and application. The preparation method has the advantages of being efficient and simple in preparation process. When the phenethyl alcohol glycoside molecular imprinting polymer is used for separating and purifying phenethyl alcohol glycoside matter in cistanche tubulosa, the process is easy to operate, and the energy consumption is low.