Radix Aucklandiae (Muxiang in Chinese), the dried root of Aucklandia lappa, is used as a medicinal material for digestive system disorders in traditional Chinese medicine for centuries. Owing to the similarity of morphologies and trade names, Radix Vladimiriae (Chuan-Muxiang), the roots of Vladimiria souliei and V. souliei var. cinerea, and Radix Inulae (Tu-Muxiang), the roots of Inula helenium and Inula racemosa, as well as the renal toxic aristolochic acid containing Radix Aristolochiae (Qing-Muxiang), the roots of Aristolochia debilis and Aristolochia contorta, are often used confusedly as the substitutes of Radix Aucklandiae. In order to ensure the effective and safe utility of Radix Aucklandiae, a GC-MS method was developed to generate the chemical profiles of essential oils of Radix Aucklandiae and its substitutes. In addition, hierarchical clustering analysis was used to compare the similarities of these chemical profiles. It was found that all the samples of A. lappa have similar chemical profiles and were clustered into one group, while the samples of Radix Vladimiriae, Radix Inulae, and Radix Aristolochiae were clustered into their own independent groups, respectively, suggesting that together with hierarchical clustering analysis, chemical profiles of essential oils generated by GC-MS could objectively discriminate Radix Aucklandiae from its common substitutes.