In this study, molecularly imprinted microfiltration membranes (MIMFMs) based on polydopamine and metal–organic framework were innovatively proposed, and successfully prepared for capturing thiamphenicol, florfenicol and chloramphenicol from milk samples through syringe filter device. The provision of PDA and coupling of MOF particles enabled the filter membranes to have great permeability and binding capacity. Cleverly, hydrophilicity and heightened rebinding selectivity (IF = 2.42) of filter membranes was provided using two functional monomers (methacrylate and acrylamide), and microfiltration-grade composite membranes were generated by adjusting the imprinting polymerization time. The combination of the selective filter membranes and the syringe filter devices can effectively simplify the operation process, minimize the extraction time and reduce the tested sample volume. The method was validated by coupling with ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) and obtained a good correlation (r2 > 0.99). The limit of detection (LOD) of three analytes was 0.0800–0.6583 µg kg−1 and the mean recovery ranged from 85.5% to 91.2% within relative standard deviations (RSDs) less than 8.2%. Finally, an effective MIMFMs-UHPLC-MS/MS method was established for the recognition and detection of three amphenicol antibiotics in milk samples. The MIMFMs filtration technique offered in this work provides valuable science references and potential application prospects for complicated sample pretreatment.