The invention discloses a magnetic covalent organic framework nanocomposite material and a preparation method and application. The method comprises the steps that by means of a solvothermal reaction method, ferroferric oxide nanoparticles, 1,3,5-tris(4-aminophenyl)benzene and terephthalaldehyde serve as the raw materials, and the magnetic covalent organic framework nanocomposite material capable of being used for separating and enriching peptide fragments with benzene ring structures or hydrophobic peptide fragments is prepared under the catalytic action of acetic acid. The preparation process is simple and effective, reagent consumption is low, and the yield is high; the obtained magnetic covalent organic framework nanocomposite material not only has the advantages of covalent organic framework materials of being porous, stable in structure, large in specific surface area and the like, but also has the advantages of magnetic materials of being good in dispersity, easy to separate, good in magnetic inductivity and the like, and the magnetic covalent organic framework nanocomposite material has a good application prospect in the fields of proteomics, peptideomics and the like.