The chromatographic fingerprint was established for evaluating and controlling the quality of germplasm resource of Ophiopogon japonicus in Sichuan Basin by reversed-phase high performance liquid chromatography and gas chromatography mass spectrometry. The results showed that each sample the characterized by the peak area of 28 HPLC peaks and 13 GC peaks in each program and these peaks were employed for hierarchical cluster analysis. Furthermore, the discrimination of the sample from different regions was achieved by hierarchical cluster analysis via recognizing the 16 (41 datamatrix. This was the first report of hierarchical cluster analysis of the wild germplasm resource of Ophiopogon japonicus according to their chemical fingerprints. Thus, the results proved it is a simple, rapid and accurate method suitable for the quality control of the traditional Chinese medicines.