A method based on stop-flow two-dimensional liquid chromatography coupled with electrospray ionization mass spectrometry (2D LC-ESI MS) was established and applied to analyze triterpenoid saponins from the main root of ginseng. Due to the special structure of triterpenoid saponins (they contain polar sugar side chains and nonpolar aglycones), hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) were used for the two dimensions, respectively. A trap column was used to connect the two dimensions. The dilution effect, which is one of the main shortcomings of traditional comprehensive 2D LC methods, was largely avoided. The peak capacity of this system was 747 and the orthogonality was 56.6 %. Compared with one-dimensional HILIC or RP LC MS analysis, 257 and 185 % more mass spectral peaks (ions with intensities that were higher than 1,000) were obtained from the ginseng main root extracts, and 94 triterpenoid saponins were identified based on MS(n) information and summarized aglycone structures. Given its good linearity and repeatability, the established method was successfully applied to classify ginsengs of different ages (i.e., years of growth), and 19 triterpenoid saponins were found through statistical analysis to vary in concentration depending on the age of the ginseng.