An innovative sandwich-structural Fe-based metal-organic framework magnetic material (FeO@SW-MIL-101-NH) was fabricated using a facile solvothermal method. The characteristic properties of the material were investigated by field emission scanning electron microscopy, transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction, vibrating sample magnetometry, and Brunauer-Emmett-Teller measurements. FeO@SW-MIL-101-NH is associated with advantages, such as robust magnetic properties, high specific surface area, and satisfactory storage stability, as well as good selective recognition ability for chlorogenic acid (CA) and its metabolites via chelation, hydrogen bonding, and π-interaction. The results of the static adsorption experiment indicated that FeO@SW-MIL-101-NH possessed a high adsorption capacity toward CA and its isomers, cryptochlorogenic acid (CCA) and neochlorogenic acid (NCA), and the adsorption behaviors were fitted using the Langmuir adsorption isotherm model. Then, a strategy using magnetic solid-phase extraction (MSPE) and ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF MS) was developed and successfully employed for the selective pre-concentration and rapid identification of CA metabolites in rat plasma, urine, and feces samples. This work presents a prospective strategy for the synthesis of magnetic adsorbents and the high-efficiency pretreatment of CA metabolites.