Abstract: Sophorae Flavescentis Radix is the dried root of Sophora flavescens Ait. and Sophorae Tonkinensis Radix et Rhizoma is the dried root and rhizome of Sophora tonkinensis Gagnep. The two drugs are both from the same genus Sophora, having similar and different compositions and efficacies, however, their differences are not fully demonstrated in current standard. In this study, the high-performance thin-layer chromatography with multi-dimensional and multi-level features combined with electric spray mass spectrometry (HPTLC-ESI-MS) was used to discover and identify the characteristic zones in extracts of Sophorae Flavescentis Radix and Sophorae Tonkinensis Radix et Rhizoma, after optimizing the preparation method of the test solution and chromatographic parameters. As a result, 17 main characteristic zones were found on HPTLC chromatograms of Sophorae Flavescentis Radix and Sophorae Tonkinensis Radix et Rhizoma, among them, besides 3 known chemicals, another 12 unknown components were identified by HPTLC-ESI-MS, they are 1 alkaloid and 11 flavonoids. The identification results were verified by the reference standards partially and nuclear magnetic resonance spectra after guided-isolation. Finally, a unified HPTLC specific identification method with different markers was established to identify Sophorae Flavescentis Radix and Sophorae Tonkinensis Radix et Rhizoma simultaneously. Thanks to abundant chemical information provided when using diverse polarity mobile phases and derivatization reagents, the HPTLC technology offers a convenient strategy for discovery, quality evaluation, and identification of target chemicals when connecting with mass spectrometry.