The invention discloses a preparation method of a magnetic nanometer molecular imprinting composite material related to estrogen, comprising the following steps: dissolving bivalent iron salt and trivalent iron salt into water, performing ultrasonic dispersion, heating and regulating the system till being alkali, stirring the system, performing magnetic separation, washing the system till that pH is 6-8, and drying the system; adding ethanol solution, performing heating, stirring and dropping oleic acid, performing magnetic separation, washing the system till that pH is 7.0, and drying the system; adding a dispersant, a polymerization monomer, a functional monomer and a cross linker, and performing ultrasonic dispersion; adding an initiator, performing heating, stirring and magnetic separation, washing the system till that pH is 6-8, and drying the system; adding a composite reaction liquid of a template molecule and amino functional reagent, performing heating, stirring and magnetic separation, washing the system till that pH is 6-8, and drying the system to obtain a target product. The preparation method has the advantages of simple preparation process, controllable magnetic content, controllable functional group proportion and so on, and can arrive at a high enrichment factor when being applied in residual trace phenol environmental estrogens in enrichment drinking water.