A novel imine-linked magnetic covalent organic polymer, Fe3O4@TAB-TFPT, was synthesized using environmentally friendly deep eutectic solvents as the reaction medium instead of conventional organic solvents. The materials were characterized by scanning electron microscope (SEM), transmission electron microscopy (TEM), FT-IR, N2 adsorption-desorption isotherms, energy dispersive spectrometer (EDS), X-ray photoelectron spectra (XPS), and thermo gravimetric analysis (TGA). Subsequently, the materials were employed as an adsorbent for magnetic solid-phase extraction (MSPE) of flavonoids, including Kurarinone, Norkurarinone, Xanthohumol, and Isoxanthohumol, prior to their determination by HPLC-MS/MS. The validation results demonstrate good linearity within the concentration range 0.1-1000ng∙mL-1 (R2 ≥ 0.9963), high enrichment factors ranging from 18.9 to 30.7, and low LODs (0.01-0.05ng∙mL-1) and LOQs (0.05-0.1ng∙mL-1). Furthermore, recoveries between 80.60% and 108.40% with relative standard deviations ≤ 8.49% were achieved. The proposed MSPE-HPLC-MS/MS method was successfully applied to the determination of flavonoids in Sophora flavescens Aition sample.