The invention provides a novel loading method of zeolite-like imidazole ester skeleton structural materials (ZIFs) on a silicon substrate and an application of the prepared material. The silicon substrate such as silicon spheres, ordered mesoporous silicon SBA-15, CMC-41, CMC-48, KT96, chromatography silica gel, capillary and the like is activated, then the activated silicon substrate is derivated, and the surface of the substrate is allowed to contain groups coordinated with metal ions; then a corresponding metal salt and imidazole are respectively dissolved in water, methanol, DMF, THF and other polar solvents to form clarified uniform solutions, and the ZIFs are grafted on the outer surface of the silicon substrate or in pore passages by a layer-by-layer self-assembly method. The invention provides the preparation method of the silicon-based ZIFs loaded material having the advantages of no needing of high temperature and high pressure treatment, stable and uniform loading and controllable thickness. The material prepared by the method has important application potential in the aspects of separation and analysis, adsorption, enrichment, purification and the like.