Molecular imprinting polymers (MIPs) are synthetic materials having specific cavities tailored for a target molecule. Thoroughly understanding the molecular recognition mechanism is favorable for the rational design, preparation, and application of MIPs. In this work, theophylline (THO)-imprinted poly(acrylonitrile-co-acrylic acid) (PANCAA) films with acrylic acid (AA) as the functional monomer were fabricated and a set of concentration-dependent Fourier transform infrared (FT-IR) spectra were collected. Two-dimensional (2D) correlation analysis of the spectra and density functional theory (DFT) calculation were conducted to evaluate the molecular recognition mechanism. DFT at the B3LYP/6-31+G(d,p) level is efficacious to calculate the binding energies (Delta E) and the theoretical vibration frequencies for the possible configurations of THO_AA complexes. An optimized cyclic hydrogen-bonded configuration (complex THO_AA1) has the highest binding energy (-16.63 kcal mol(-1)) that is more stable than others. In addition, the experimental vibrations of the carbonyl groups in the FT-IR spectra were assigned on the basis of the DFT results. Moreover, methylacrylic acid (MAA) and caffeine (CAF) as compared analogues were also investigated. The DFT-based theoretical predictions are coincident with the reported results.