A molecularly imprinting polymer (MIP) was synthesized via bulk polymerization under different conditions using anti-ague drug cinchonine (CN) as template. Infrared spectra (IR) results show that the template CNand functional monomer α-methyl acrylic acid (MAA) formed complexes before polymerization and the structure of complexes was simulated by Hyperchem. The results indicate that there are hydrogen bond or ionic bond between functional monomer and template molecule in acetonitrile solution. The MIP made in cold-initiated photo-polymerization has higher separation performance than that in the therm-initiated polymerization. The separation of the isomers CN and cinchonidine (CD) can be successfully obtained when its separate factor α reaches 1.82. Scatchard analysis suggests that the MIP recognizing CN with two classes of binding sites. The partition coefficient Kd, 1 and apparent maximum number nmax, 1 of binding sites with high affinity are 131.43 μmol/L and 58. 90 μmol/g, respectively,while Kd, 2 and nmax, 2 of binding sites with low affinity are 2.32 mmol/L and 169.08 mmol/g, respectively.