The Fritillaria genus, including different kinds of medicinal and edible plants belonging to the Liliaceae family which have the function of treating and relieving a cough and eliminating phlegm, is widely planted in Xinjiang (China). There are few comprehensive studies reporting on the characterization of the chemical constituents of Fritillaria from Xinjiang, and to date, no work describing the quantitative differences between the components in Fritillaria from Xinjiang and related species. The purpose of this study was to develop qualitative and quantitative analytical methods by Ultra Performance Liquid Chromatography-Quadrupole Time-of-flight Mass Spectrometry (UPLC-QTOF-MS) for the rapid quantification and quantitation of alkaloids in wild and cultivated Xinjiang Fritillaria, which could be used in the quality control of medicine based on this natural herb. Using the UPLC-QTOF-MS method, the chemical constituents of Xinjiang Fritillaria were identified by fragmentation information and retention behavior, and were compared to reference standards. Furthermore, a quantitative comparision of four major alkaloids in wild and cultivated Xinjiang Fritillaria was conducted by determining the content of Sipeimine-3β-d-glucoside, Sipeimine, Peimisine, and Yibeinoside A, respectively. A total of 89 characteristic peaks, including more than 40 alkaloids, were identified in the chromatographic results of Fritillaria. Four main alkaloids were quantified by using a validated method based on UPLC-QTOF-MS. The relative contents of Sipeimine-3β-d-glucoside, Sipeimine, Peimisine, and Yibeinoside A varied from 0.0013%~0.1357%, 0.0066%~0.1218%, 0.0033%~0.0437%, and 0.0019%~0.1398%, respectively. A rough separation of wild and cultivated Fritillaria could be achieved by the cluster analysis method.