High-performance liquid chromatographic (HPLC) fingerprints of 12 authentic samples and 26 commercial samples of Fructus Aurantii Immaturus (FAI) from different sources of China were measured. Firstly, the main bioactive compounds in citrus herb, namely naringin and hesperidin, were identified and quantitated. Then, principal components analysis (PCA) was performed to differentiate and classify the studied samples based on the principal peaks and entire chromatograms, respectively. Hierarchical clustering analysis (HCA) and similarity analysis (SA) were further conducted to validate the clustering results. The optimized HPLC-DAD method aided by forementioned chemometric methods shows that the chemical fingerprints of 38 samples from extensive sources could be reasonably identified and systematically analyzed, which offers a new clue for the study of traditional Chinese medicines (TCM). The results obtained will provide a useful foundation for quality control of herbal medicine.