Codonopsis Radix (CR) is often used as both a medicine and a food ingredient. However, identifying CR can be difficult due to various factors such as variety, sulfur fumigation, and storage time. Consequently, a comprehensive strategy based on fingerprinting and chemometric approaches was developed to distinguish different CRs. First, the fingerprints of CR were acquired by high‐performance liquid chromatography (HPLC). Secondly, various chemical pattern recognition methods were employed to identify CR. Additionally, 14 and 16 major compounds were identified as marker compounds to differentiate between different varieties and sulfur‐fumigated samples, respectively. Furthermore, the amount of Lobetyolin present in different samples was determined, showing that the content of Lobetyolin varied significantly across the samples. Codonopsis pilosula Nannf. var. modesta (Nannf.) L.T.Shen had the highest content of Lobetyolin, followed by Codonopsis tangshen Oliv., and Codonopsis pilosula (Franch.) Nannf. In addition, the content of Lobetyolin was highest when it was non‐sulfur‐fumigated and stored for 0 years. Conclusively, HPLC fingerprint in conjunction with chemical pattern recognition and component content determination, can be employed to differentiate different varieties and sulfur‐fumigated CR. Additionally, it is a reliable, comprehensive, simple, and rapid method for the identification of CR.