The invention provides a three-dimensional bionic nanometer material for capturing circulating tumor cells and a preparation method thereof.The material is composed of porous graphene, microballoon spheres and a silicon substrate, a three-dimensional array structure is formed through electrostatic adsorption and self-assembly, chemical modification is carried out on the surfaces of the graphene and the microballoon spheres, E-selectin protein molecules and ligands used for cell capturing are modified and fixed, and a bionic structure for enhancing cell recognition is achieved.The material can be integrated in a micro-fluidic chip, recognition and capturing of the chip for the circulating tumor cells is are enhanced, separation efficiency is improved, and the captured cells can be detected and analyzed conveniently; a fixed recognition ligand is changed, the material can also be used for effectively capturing different types of cells, and rare tumor cells can be recognized and captured from peripheral blood samples.