Background: Mugua is a common Chinese herbal medicine. There are three main medicinal origin places in China, Xuancheng City Anhui Province, Qijiang District Chongqing City, Yichang City, Hubei Province, and suitable for food origin places Linyi City Shandong Province. Objective: To construct a qualitative analytical method to identify the origin of medicinal Mugua by near infrared spectroscopy (NIRS). Materials and Methods: Partial least squares discriminant analysis (PLSDA) model was established after the Mugua derived from five different origins were preprocessed by the original spectrum. Moreover, the hierarchical cluster analysis was performed. Results: The result showed that PLSDA model was established. According to the relationship of the origins-related important score and wavenumber, and K-mean cluster analysis, the Muguas derived from different origins were effectively identified. Conclusion: NIRS technology can quickly and accurately identify the origin of Mugua, provide a new method and technology for the identification of Chinese medicinal materials.