The invention relates to a method for observing microscopic structures inside plant roots, which is capable of effectively solving the problem of utilizing a microscope to clearly observe the structures inside the plant roots. The method comprises the steps of digging out the plant roots, washing, shearing the plant roots into small sections, fixing the plant roots by methanol, and then embedding by a sepharose solution, cooling, condensing, trimming into small blocks, after freehand section, placing the small blocks into distilled water in a container, performing lactic acid clearing, covering, dyeing via berberine or fluorescein, bleaching by the water, performing poststaining via toluidine blue O or sarranine O, bleaching by the water, performing water seal, observing and photographing via an inverted fluorescence microscope, and obtaining a clear image. The method can be used for observing the microscopic structures inside the plant roots, thereby being effectively used for the research on classification, auxanology, ecology and physiology of medical plants. The method disclosed by the invention has the advantages of simple method, easiness in operation, low cost, low working capacity, high success rate, and good effect, thereby being capable of being used for the research on morphological anatomy of the roots. The method is simpler and more effective for the thinner root sections of the plants.