Previous studies have unraveled that gypenosides produced from Gynostemma pentaphyllum (G. pentaphyllum) are mainly damarane triterpenoid saponins with diverse structure and important biological activities, but the diversity mechanism of gypenosides biosynthesis is still unclear. In this study, combination of iTRAQ proteome analysis and RNA sequencing transcriptome analysis was applied to detect the proteins and genes related to gypenosides biosynthesis. 3925 proteins were identified by proteomic sequencing, of which 2537 were quantified. 17 cytochrome P450 (CYP) and 11 UDP glycosyltransferase (UGT) candidate genes involved in the side chain synthesis and modification of gypenosides were found.