The invention relates to a method for preparing a conductive polymer based electromagnetic composite material. The method comprises the following steps of: respectively preparing magnetic powder suspending liquid, monomer dispersion liquid and an initiator solution, filling the magnetic powder suspending liquid, the monomer dispersion liquid and the initiator solution into three injectors, and continuously injecting the magnetic powder suspending liquid, the monomer dispersion liquid and the initiator solution into respective microtubules at a constant pushing speed respectively; mixing the reaction solutions in a reaction tube after the reaction solutions flow through the microtubules, and performing fluid reaction polymerization at room temperature under ultrasound assistance; and performing magnetic separation, washing, and freeze-drying on the product to obtain the conductive polymer based electromagnetic composite material. The method is simple, low in energy consumption, good in repeatability, capable of realizing continuous and fast preparation of the product, and easy to realize industrial production; and the prepared conductive polymer based electromagnetic composite material is uniform in particle size, large in specific area, stable in physical and chemical properties, difficult to agglomerate, good in dispersity and excellent in electromagnetic comprehensive performance, and has a good application prospect.