The invention discloses a method for extracting active sites of iridoid, and extracting monomer geniposidic acid (GPA), geniposide(GP) and aucubin(AU) from eucommia, wherein raw materials are extracted by taking the eucommia(husk, leaf or seed) as materials and utilizing the conventional leaching method, the ultrasonic extraction method or the microwave extraction method, and an extracting solution is preliminarily purified by methods such as the solvent extraction and the adsorption separation of special adsorbents, etc., and thus the active sites of the iridoid(the total content of the iridoid is no less than 50 percent) is obtained, and GPA, GP and AU undergo the separation, low temperature condensation, refrigeration and drying by using the preparation high pass filter technique and taking an alcohol-water solution as the mobile phase to obtain monomers of GPA, GP and AU, contents of which are all no less than 90 percent. The preparation method disclosed by the invention utilizes novel process of the extraction and separation, and can simultaneously prepare a plurality of monomer products of the eucommia, and provides scientific foundations for the comprehensive development and utilization of the eucommia; moreover, the whole process does not use solvents harmful to human bodies, thereby realizing the green preparation.