Introduction: The tuberous roots of Stephania kwangsiensis, which contain bioactive alkaloids, are used as a traditional Chinese medicine. Overexploitation of the roots has made the plant increasingly rare, and the abundant leaves of the same plant may offer a potential alternative. However, there is insufficient phytochemical information for a comparison of alkaloid compositions in the two parts. Objective: To characterise and compare the alkaloids in the leaves and roots of S. kwangsiensis. Methods: The alkaloids in S. kwangsiensis were characterised using high pressure liquid chromatography coupled with positive electrospray ionisation quadrupole time-of-flight tandem mass spectrometry (HPLC-(+)ESI-QTOF-MS/MS). The alkaloid compositions in the leaves and roots were compared by visual inspection combined with principal component analysis (PCA) of the HPLC-MS data. Results: Seventy-five alkaloids comprising aporphine-, proaporphine-, protoberberine-, benzylisoquinoline-, bisbenzylisoquinoline- and morphine-type alkaloids were identified or tentatively identified in the roots and leaves of S. kwangsiensis. Sixty-three of these alkaloids have not been previously reported in this species, and three have not been previously reported in the literature. The roots and leaves had similarities in alkaloid composition but differences in the peak intensities of most alkaloids. The PCA revealed that the samples were clustered into two distinct groups, which corresponded to leaves and roots. Conclusion: This study further clarified the chemical constituents in the roots of S. kwangsiensis, and revealed that diverse alkaloids were also present in the leaves. The comparative chemical profiling of the two parts provides useful information on their potential medicinal use. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.