The present invention provides a method for preparing 20-O-β-D-glucopyranosyl-20(S)-protopanaxadiol (Ginsenoside M1) by using Sanqis leaves and stems. The method of the invention includes the steps of: (a) provides powder of Sanqi leaves and stems; (b) provides a fungus for fermenting the Sanqi leaves and stems, wherein the fermentation temperature is ranged from 20-50° C., the fermentation humidity is ranged from 70-100%, the pH value is ranged from 4.0-6.0, and the fermentation period is ranged from 5-15 days; (c) extracts and collects the fermentation products; and (d) isolates 20-O-β-D-glucopyranosyl-20(S)-protopanaxadiol from the fermentation products.