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Objectives The purpose of this paper was to construct a reliable methodology to discriminate the geographical origins of Chuanminshen violaceum Sheh et Shan planted in different regions in Sichuan, China. Materials and methods Fatty acid profiles of roots and leaves of C. violaceum planted in various regions of Sichuan Province in China, namely Guangyuan (GY), Langzhong (LZ), Jintang (JT), Bazhong (BZ), and Shuangling (SL), were determined using GC-MS followed by multivariate statistical analyses, including orthogonal partial least-squares discriminant analysis and hierarchical clustering analysis. Results Leaves of C. violaceum showed the highest contents of hexadecatrienoic acid (3.21 g/kg), linoleic acid (6.62 g/kg), and α-linolenic acid (7.24 g/kg), which were all higher than those contained in roots. Chuanminshen violaceum samples collected from LZ, JT, and GY could be clearly distinguished based on fatty acid profiles of leaves and those collected from LZ, GY, and BZ could be clearly distinguished based on fatty acid profiles of roots. Conclusions Chemometric method is used as a potential approach for analyses of fatty acid profiles of roots and leaves to control the quality of C. violaceum and their powered products.