Abstract: OBJECTIVE To establish a UHPLC-Q-TOF-MS/MS method to analysis the metabolic profiles of flowers, leaves, stems and bulbs of Fritillaria thunbergii Miq., and study the difference of chemical composition in different parts. METHODS Samples were extracted and the separation of the analytes was carried out on the UPLC BEH Amide column(2.1 mm×100 mm, 1.7 μm) using the mobile phase of water(containing 25 mmol·L^-1 of ammonium acetate-25 mmol·L^-1 of ammonia) and acetonitrile by gradient elution. The detection was performed in the electrospray ionization positive mode. Through the analysis of the multistage tandem mass spectrometry, the characteristic peaks were extracted with mass spectrometry data peak matching, peak alignment, noise filtering. Principal component analysis and orthogonal partial least squares discriminant analysis were used to analyze the data. RESULTS The 113 chemical constituents were identified. The results of principal component analysis showed that the flowers, bulbs, stems and leaves of Fritillaria thunbergii Miq. could be obviously divided into four categories, indicating that there were significant differences in chemical components from different parts. The orthogonal partial least squares discriminant analysis results showed that the differential compounds between the flowers and the stems, bulb, leaves of Fritillaria thunbergii Miq. were 16, 19 and 12, respectively. Among them, the contents of isoamyl adenine nucleoside, prolyl aspartic acid, anti-zein and ethyl amine were higher in the flowers. CONCLUSION This study establish a fast, accurate, and reliable method for differentiating the different parts of Fritillaria thunbergii Miq.. Moreover, this study provides a scientific basis for the comprehensive development and utilization of Fritillaria thunbergii Miq.