The invention discloses a method for preparing radix ginseng/radix panacis quinquefolii extract by applying microorganism through quick fermentation. The method comprises the following steps: (1) carrying out sterilizing, washing and drying treatment on radix ginseng/radix panacis quinquefolii, thus obtaining cleansing radix ginseng/radix panacis quinquefolii; (2) superfinely smashing the cleansing radix ginseng/radix panacis quinquefolii into superfine powder, thus obtaining radix ginseng/radix panacis quinquefolii superfine powder; (3) adding a carbon source, a nitrogen source and water in the radix ginseng/radix panacis quinquefolii superfine powder, uniformly stirring, and inoculating probiotics and saccharomycetes, thus obtaining a fermentation material; (4) fermenting the fermentation material for one hour or more at the constant temperature of 45 to 55 DEG C; (5) carrying out sieving treatment on a fermented mixture after completing fermentation, thus obtaining a radix ginseng/radix panacis quinquefolii enzyme solution, i.e., the radix ginseng/radix panacis quinquefolii extract. According to the method disclosed by the invention, the content of effective components of the extracted radix ginseng/radix panacis quinquefolii extract is high, the production period is short, and automatic production can be realized.