The invention provides super macroporous polymer microspheres and a preparation method thereof. The preparation method comprises the following steps of: firstly, preparing an oil-in-water in-water composite emulsion as a template for super macroporous microspheres through a two-step emulsion process; then, solidifying an oil phase by using a solvent removal method to form super macroporous microspheres provided with inner-outer through pore passages; and finally, after molding the microspheres, further crosslinking microsphere skeleton molecules to obtain microspheres with rigid resin structures. The microspheres prepared by the method have a through pore passage structure, the controllable particle size range is 0.1-300 microns, the controllable pore size range is 0.09-90 microns, and the controllable porosity range is 10-90%. Super macroporous structures are beneficial for biological macromolecules to penetrate through and enter the microspheres, the mass transfer by convection in the microspheres can be realized, and the rigid structure can tolerate higher pressure and higher flow velocity. The super macroporous polymer microspheres can be used as stationary phase fillers for chromatographic separation, immobilized carriers of enzymes, cell culture micro-carriers, tissue engineering micro scaffold materials, adsorbing materials and the like.