A comprehensive off-line two-dimensional liquid chromatography (2D-LC) method coupling hydrophilic interaction liquid chromatography (HILIC) and reversed phase liquid chromatography (RPLC) was developed in this study to detect as many saponins as possible in extracts of Panax notoginseng. The orthogonality of the 2D HILIC × RPLC was up to 81%, and the peak capacity was 10200. In total, 224 saponins were found, and some of them were trace amounts. Besides, a screening table designed by adding molecular weights of possible aglycones and sugars was constructed to help rapidly characterize the saponins using MS information. Unfortunately, the structure of saponins could not be identified by using only MS information.