Carbamazepine (CBZ) is a typical pharmaceutical residue commonly found in aqueous environments, but its removal through activated carbon or advanced oxidation processes is often disrupted by co-existing organic matter. An imprinting system which consisted of the target pollutant CBZ (template molecule) and 10 different kinds of functional monomers was constructed via molecular simulation to screen for appropriate monomers, thereby addressing CBZ removal disruptions. An annealing method simulation was used to search for stable, low-energy conformations of the template-monomer interaction system to calculate the binding energy of these different monomers with CBZ. The order of binding affinity calculated was: 4-vinylbenzoic acid > itaconic acid > methacrylic acid, which was consistent with the experimental observations. The adsorption capacity of the molecular imprinted polymer (MIP) prepared using 4-vinylbenzoic acid reached 28.40 mg/g, and the imprinting factor reached 2.72. The simulation and measurement of the ultraviolet spectrum of the imprinting system showed that a new interaction system was formed between the template and monomers, and that multiple binding conformations between them took place when specific recognition occurred. Energy calculation and hydrogen bond analysis revealed that the van der Waals force, including the π-π conjugate and electrostatic forces including hydrogen bonding, played an important role during selective adsorption, which was confirmed by infrared spectroscopy analysis.