In this study, a highly efficient magnetic molecularly imprinted polymer nanocomposite material was prepared using multi-walled carbon nanotubes as carriers. The characterization of the obtained nanocomposite material was conducted using Fourier transform infrared spectroscopy, a vibrating sample magnetometer, a thermogravimetric analyzer, a scanning electron microscope, and a transmission electron microscope. The adsorption properties of the nanocomposite material were evaluated through adsorption experiments, including static adsorption, dynamic adsorption, and selective recognition studies. The prepared nanocomposite material, serving as a selective adsorbent, was applied in magnetic solid-phase extraction. Subsequently, the derivatized samples were analyzed for glucose in fish serum using liquid chromatography–tandem mass spectrometry. Under optimal conditions, the detection limit was 0.30 ng/mL, the quantitation limit was 0.99 ng/mL, satisfactory spiked recovery rates were obtained, and the relative standard deviation was less than 1.1%. Using 2-deoxy-D-ribose as the template molecule and a structural analog of glucose allowed us to eliminate the potential template leakage in qualitative and quantitative analyses, effectively avoiding the issues of false positives and potential quantitative errors, compared to traditional methods. A method for detecting glucose levels in fish serum based on molecularly imprinted polymer technology has been successfully developed to determine the stress and health levels of fish.