The present invention relates to a method for selectively preparing ginsenoside F2, compound Mc and compound O, which originally exist in ginseng at low levels, from saponin of ginseng, and specifically, to a method for obtaining desired and targeted compound, in other words, ginsenoside F2, compound Mc and compound O with a high yield, by treating a specific enzyme to saponin obtained from ginseng and structure converting the saponin.COPYRIGHT KIPO 2017