Echinacea purpurea (EP) is a common medicinal material for extracting anti-RSV components. However, up to now, there has been no effective and simple method to comprehensively reflect the quality of EP. In our current study, the quality of Echinacea purpurea (L.) Moench samples from six different cultivation locations in China was evaluated by establishing a high-performance liquid chromatography (HPLC) fingerprint, combining chemical pattern recognition and multi-component determination. In this study, the chemical fingerprints of 15 common peaks were obtained using the similarity evaluation system of the chromatographic fingerprints of traditional Chinese medicine (2012A Edition). Among the 15 components, three phenolic acids (caftaric acid, chlorogenic acid and cichoric acid) were identified and determined. The similarity of fingerprints of 16 batches of Echinacea purpurea (L.) Moench samples ranged from 0.905 to 0.998. The similarity between fingerprints of five batches of commercially available Echinacea pupurea (L.) Moench and the standard fingerprint ”R” ranged from 0.980 to 0.997, which proved the successful establishment of the fingerprint. PCA and HCA were performed with the relative peak areas of 15 common peaks (peak 3 as the reference peak) as variables. Anhui and Shaanxi can be successfully distinguished from the other four cultivation areas. In addition, the index components of caftaric acid, chlorogenic acid and cichoric acid were in the range of 1.77–8.60 mg/g, 0.02–0.20 mg/g and 2.27–15.87 mg/g. The results of multi-component index content determination show that the contents of the Shandong cultivation area were higher, followed by Gansu, Henan and Hebei, and the lowest were Anhui and Shaanxi. The results are consistent with PCA and HCA, which proved that the quality of Echinacea purpurea (L.) Moench from different origins was different. HPLC fingerprint combined with chemical pattern recognition and multi-component content determination was a reliable, comprehensive and prospective method for evaluating the quality of Echinacea purpurea (L.) Moench. This method provides a scientific basis for the quality control and evaluation of Echinacea purpurea (L.) Moench.