The purpose of this study is to develop a new preparation process of Notoginseng root(Panax notoginseng) extracts having high concentrations of ginsenoside $Rg_3$, $Rg_5$, $Rk_1$ and $Rh_4$, a special component of Red and Black ginseng(Panax ginseng). Chemical transformation from ginseng saponin to prosapogenin was analyzed by the HPLC. Extracts of Notoginseng root was processed under several treatment conditions including microwave and vinegar(about 14% acidity) treatments. Results of those treatments showed that the quantity of ginsenoside $Rg_3$ increased by over 7.6% at 15 minutes of pH 2~4 vinegar and microwave treatments. The results of processing with MPN-15 indicate that the microwave and vinegar(about 14% acidity) processed Notoginseng root extracts that had gone through 15-minute treatments were found to contain the largest amount of ginsenoside $Rg_3$(7.639%), $Rg_5$(6.061%), $Rk_1$(1.516%) and $Rh_4$(1.599). It is thought that such results provide basic information in preparing Notoginseng root extracts with functionality enhanced.