The invention discloses a method for preparing rare ginsenoside by hydrolyzing ginsenoside with acidic amino acid. Panoxadiol saponins are converted to generate 20R-Rg3, 20S-Rg3, Rg5 and Rk1, and panaxatriol saponins are converted to generate Rg6, F4, Rk3 and Rh4. Compared with an existing preparation process, the hydrolysis capacity of acidic amino acid is more than 10 times of that of neutral amino acid and that of basic amino acid and can better meet requirements of industrial preparation of rare ginsenoside, the defects that the hydrolysis specifity of ginsenoside is poor, the yield is low, the corrosion is high, environment pollution is caused, multiple byproducts are produced and the like due to the fact that a large amount of strong acid and strong base are used are overcome, ginseng resources are fully used, rare ginsenoside is extracted and enriched to the largest extent, the purpose of simple, quick, environment-friendly and low-cost enrichment of rare ginsenoside is achieved, and the method guarantees industrial production and preparation of new medicines.