In the study, four different semiempirical algorithms, modified neglect of diatomic overlap, a reparameterization of Austin Model 1, complete neglect of differential overlap and typed neglect of differential overlap, have been applied for the energy optimization of template, monomer, and template-monomer complexes of imprinted polymers. For phosmet-, estrone-, and metolcarb-imprinted polymers, the binding energies of template-monomer complexes were calculated and the docking configures were assessed in different molar ratio of template/monomer. It was found that two algorithms were not suitable for calculating the binding energy in template-monomers complex system. For the other algorithms, the obtained optimum molar ratio of template and monomers were consistent with the experimental results. Therefore, two algorithms have been selected and applied for the preparation of enrofloxacin-imprinted polymers. Meanwhile using a different molar ratio of template and monomer, we prepared imprinted polymers and nonimprinted polymers, and evaluated the adsorption to template. It was verified that the experimental results were in good agreement with the modeling results. As a result, the semiempirical algorithm had certain feasibility in designing the preparation of imprinted polymers.