The invention relates to a preparation method of covalent organic framework composite microspheres with core-shell structures. The method comprises the following steps: dissolving silicon dioxide microspheres, a first construction element and a second construction element in an organic solvent; and after adding a catalyst, rapidly synthesizing into the composite microspheres with core-shell structures at a certain temperature. In a preparation process, reaction conditions are gentle, the method is simple, and the yield is high; the prepared covalent organic framework composite microspheres have the advantages of good core-shell morphology, high specific surface area, ordered pore structures, good mechanical stability, thermal stability, chemical stability and the like, if the microspheres are used as a chromatographic stationary phase, the chromatographic mass transfer resistance can be reduced effectively, the theoretical plate height is improved, and finally, column efficiency and degree of separation are improved; and if the microspheres are used as solid-phase extracting filler, the enrichment effect can be improved remarkably. The covalent organic framework composite microspheres with core-shell structures have good application prospects in the aspect of separation and enrichment of small organic molecules.