In this study, surface molecularly imprinted polymers were synthesized with the metal-organic framework NH2-MIL-53 as carrier and naringenin as alternative template of Ochratoxin A (OTA). The amino groups on the surface of NH2-MIL-53 reacted with the epoxy groups in glycidyl methacrylate (GMA). Subsequently, the double bonds of the GMA grafting on the surface of the material were used for polymerization to prepare the surface molecularly imprinted polymers. The obtained polymers were characterized by scanning electron microscope, transmission electron microscope, energy spectrometer, Fourier infrared spectrometer, X-ray diffraction, and laser particle size analyzer. Synthetic polymer was combined with solid phase extraction for separation and enrichment of trace OTA in grains. The spiked recoveries were found to be 78.95–106.45%, with relative standard deviations ranging from 5.16% to 6.31%. The detection limit and the quantification limit of the method were 0.04 µg·kg−1 and 0.12 µg·kg−1, respectively. Comparing the pretreatment effects of the self-made cartridge and the immunoaffinity column on the OTA in the sample, it showed that the self-made column had excellent performance and provided a new pretreatment method for the treatment of OTA in grains.