The invention discloses maca superfine powder as well as a preparation method and application thereof. The grain size of the maca superfine powder is measured by a dry method laser granulometry meter and is 0.5-3 micrometers. The preparation method of the powder comprises the following steps: 1 removing impurities and cleansing; 2 freeze-drying, and carrying out sterilization treatment after drying; 3 grinding dry maca powder into coarse powder, then carrying out superfine-grinding in a jet mill, and thus obtaining the superfine powder with the grain size being 0.5-3 micrometers. The conditions of superfine-grinding are as follows: the grinding temperature is 18-25 DEG C, the pressure of a superfine-grinding machine when the powder enters the superfine-grinding machine is 1.5-3Mpa, the grinding pressure is 3-7Mpa, the airflow velocity is 190-300m/s, and the grinding time is 1-3h. The maca superfine powder is used for treating low immunity, physical fatigue and sexual dysfunction and has the advantages of being significant in curative effect and stable in condition of patients, improving the survival quality of patients, increasing the weight of patients, improving the immunologic function of patients, and being safe in medication.