Ce-doped Fe3O4 magnetic particles (Ce-Fe3O4 MPs) were synthesized by co-precipitation method. The coordination and adsorption properties of Ce-Fe3O4 MPs to different natural products were investigated. The results verified that the catechol-like,maltol-like and acetylacetone-like donor sets of flavonoids were the binding sites with Ce-Fe3O4 MPs. The adsorption was conformed to be pseudo-second-order model and single-layer adsorption after being characterized by adsorption kinetics and adsorption thermodynamics. The adsorption and desorption conditions were optimized. It was found that different components adsorbed on the Ce-Fe3O4 MPs surface can be selective desorbed in different solvents, which was helpful for the selective separation to adsorbed components. The Ce-Fe3O4 MPs were successfully applied to selective adsorption of compounds containing catechol-like, maltol-like and acetylacetone-like donor sets in the crude extract of Scutellaria baicalensis Georgi and Rheum palmatum L. The results demonstrated that the magnetic solid phase extraction (MSPE) method based on Ce-Fe3O4 MPs has the advantages of high structural selectivity, high efficiency and low consumption, and can be used for efficient separation of flavonoids with specific structures from natural products.