The inventeion discloses maca flower superfine powder and a preparation method thereof. The preparation method comprises the following steps: S1, drying, namely first pre-freezing maca flowers, and performing vacuum freeze drying, so that the moisture content is 3-7%; S2, coarse grinding, namely grinding the dried maca flowers into coarse powder, and standing under the condition of 0-15 DEG C; and S3, superfine grinding, namely introducing air subjected to freeze drying into the coarse powder, and obtaining the maca flower superfine powder by adopting a cell disruption superfine grinding technology, wherein the particle size of the powder is less than 10 microns. According to the invention, the defects that the traditional Chinese medicine health care products are complicated in processing, nutritive materials are lost in the processing process and the like are overcome due to the adoption of a low-temperature disruption superfine grinding method. Pigments, other additives and the like are not added in the operating process, so that the nutrition and flavor substances of the maca flower are remained to the greatest degree, the obtained maca flower superfine powder is pure, natural, safe and sanitary, the retention rate of active ingredients such as macamides, glucosinolate, adenosine, total saponins and the like is high, and the powder is uniform.