The invention relates to a method for preparing a molecular imprinted polymer on the surface of carbon microspheres, which comprises the following steps of: preparing the carbon microspheres by using acetylene gas; and preparing imprinted carbon microspheres on a three-neck flask, a water bath and an electrothermal stirring vessel, namely performing oxidation treatment on the carbon microspheres and then performing surface modification on the oxidized carbon microspheres to prepare the imprinted carbon microspheres and form irregular hole prints on the surface of the carbon microspheres. The preparation method has the advantages of advanced and reasonable process, short process flow, less environmental pollution, attractive appearance of a product, high purity of 99 percent and high product yield of 91 percent; the imprinted carbon microspheres are black and round particles with the particle diameter of 100 to 200nm and can be matched with various chemical substances; the method is anideal method for preparing the imprinted carbon microspheres; and the product can be applied to the fields of pharmacy and various industries.