A novel molecularly imprinted solid-phase extraction-ultra-performance liquid chromatography (MISPE-UPLC) method for effective separation and simultaneous determination of cyromazine, melamine, and their metabolites (ammeline and ammelide) in milk samples was developed. Molecularly imprinted polymers (MIP) were synthesized in an ethanol-water system, with melamine as the template and methacrylic acid as the organic functional monomer. The MIP were applied as a specific sorbent for the selective solid phase extraction of cyromazine, ammelide, melamine and ammeline. The molecular recognition mechanism was investigated by molecular simulation and the experiment was validate by using Fourier transform infrared spectroscopy and (1)H nuclear magnetic resonance spectroscopy. A new mechanism based on the formation of both an amido group and hydrogen bonds was developed. A binding study demonstrated that the MIP showed excellent affinity to and high selectivity for melamine and related compounds. Under optimized conditions, we achieved good linearity of the calibration curves with correlation coefficients >0.999. Low limits of quantification (LOQ) for the method were determined to be 1.25, 1.25, 2.59, and 6.42 µg/kg for cyromazine, ammelide, melamine, and ammeline, respectively, which were 3 orders of magnitude smaller than the maximum residue limit (MRL). The high sensitivity of this method allows detection at the microgram per kilogram level. The proposed MISPE-UPLC method is a highly selective and sensitive method for determination of cyromazine, melamine, and their metabolites (ammeline and ammelide) for use in the control and quality assurance of milk.