Puerariae Radix is one of the most widely used ancient traditional Chinese medicines and is also consumed as food, which has rich edible and medicinal value. Puerariae Radix can be divided into Puerariae Lobatae Radix (PL) and Puerariae Thomsonii Radix (PT). These two medicinal materials are very similar, and they are often mixed up or misused. In this study, gas chromatography–ion migration spectrometry (GC-IMS) was used to analyze the volatile organic compounds (VOCs) of PL and PT, and the differences in VOCs were analyzed using fingerprint, principal component analysis (PCA), and orthogonal partial least squares discriminant analysis (OPLS-DA). The results showed that a total of 173 VOCs were obtained from PL and PT, and 149 were qualitatively identified, including 38 aldehydes, 22 alcohols, 22 ketones, 19 esters, 13 esters, 10 acids, 10 pyrazines, 6 terpenes, 4 furans, and 2 pyridines. The characteristic VOCs of PL and PT were clarified by constructing GC-IMS fingerprints. PL and PT can be effectively distinguished, and five characteristic VOCs were screened using PCA and OPLS-DA analysis methods. This study identified and evaluated the types and differences in VOCs in PL and PT. The established method is simple, rapid, accurate, and sensitive, and it provides theoretical guidance for the identification, tracing, and quality evaluation of PL and PT.