Phase inversion molecular imprinting of theophylline (THO) was performed using acrylonitrile (AN) copolymers with acrylic acid (AA) (P(AN-co-AA)) and methacrylic acid (MA) (P(AN-co-MA). These copolymers were synthesized in the presence of the THO template at different template concentrations with [THO]/[COON] = 0.4, 1, and 2. Then, polymer solutions were casted and phase-inversed in water to prepare THO-imprinted copolymers. After template extraction, heterogeneous binding experiments of THO and its analogues caffeine, hydroxyethyl THO, uracil, theobromine, lumazine, and purine were performed. It was found that binding amounts of THO depended on [THO]/[COON]. At [THO]/[COON] = 1, THO-imprinted copolymers bound effectively to the THO substrate. Comparison was made by H-1 NMR experiments for a monomer solution with THO and copolymers prepared with and without template polymerization. Evidence showed that the template interacted with the COON proton in the monomer solution via hydrogen bonding and that template copolymerizations caused a conformation change of copolymer segments. Resultant template copolymers had selective recognition to THO, and effective imprinting of template copolymers with MA segments was observed.