An efficient method for quality control of Fructus Aurantii Immaturus (FAI), a famous traditional Chinese medicine (TCM) was established. A simple and reliable high-performance liquid chromatography-photodiode array detector (HPLC-DAD) procedure coupled with chemometric methods was developed for fingerprint analysis, qualitative analysis and quantitative determination of this herb. In qualitative and quantitative analyses, heuristic evolving latent projection (HELP) method was employed to resolve the overlapping peaks of the tested samples. Two bioactive components, namely hesperidin and naringin, are confirmed and determined, together with four flavonoids compounds tentatively identified including two new ones. From fingerprint analysis, the fingerprint data were processed with correlation coefficients for quantitative expression of their similarity and dissimilarity. The developed method based on an integration of chromatographic fingerprint and quantitative analysis is scientific, and the obtained results can be applied to the quality control of herb medicine.