The fruits of Lycium ruthenicum Murr. have long been used in folk medicine. Nevertheless, detailed information related to its phenolic composition and its quality control remains scarce. In this study, a simple and reproducible method, based on high-performance liquid chromatography combined with chemometrics, was developed to authenticate 18 samples of L. ruthenicum Murr. collected from different parts of China through fingerprint analysis. The main peaks were identified by quadrupole time-of-flight electrospray ionization mass spectrometry. Four phenolics were quantified, and the most abundant phenolic compound in almost all samples was kukoamine A. Hierarchical cluster analysis and principal component analysis were applied to classify these samples. Also, a total of 26 compounds, which were mainly phenolic compounds and anthocyanins, were identified or tentatively identified based on the available literature and standard references. Among these, 16 were reported for the first time in the extract. The results showed that there was no significant difference between L. ruthenicum fruits from different provinces in terms of chemical composition. Also, the fingerprint together with chemometric analyses and quadrupole time-of-flight electrospray ionization mass spectrometry are promising methods for evaluating the quality consistency, identification, and comprehensive evaluation of L. ruthenicum.