The invention discloses a Grifola frondosa ultramicro nutritious flour and a preparation method thereof. The method comprises the following steps: successively carrying out prefreezing, lyophilization, desorption drying and superfine crushing on the Grifola frondosa raw material, so as to obtain the Grifola frondosa ultramicro nutritious flour. The Grifola frondosa ultramicro nutritious flour provided by the invention has unique physical and chemical properties, good mobility, caking resistance and dispersion, and greatly keeps nutrients in the Grifola frondosa raw material; and ultramicro powder morphology benefits compound processing with other food raw materials, and plays an important role in improving digestion, absorption and biological utilization rate of nutrients in the Grifola frondosa. The Grifola frondosa ultramicro nutritious flour can be used as a main raw material for preparing Grifola frondosa healthful drinks, jelly and fruit juice, as well as for producing novel functional food, and can be stored for a long time.