Daodi medicinal material (DMM), which is traditional Chinese herbal medicine that has been used for long periods and have gained credibility in clinical practice, is part of the Chinese culture. However, Zhongning Goji berries (ZNG), a DMM, are illegally adulterated in the market by adding non Zhongning goji berries (NZNG). Consequently, the development of biomarker(s) is necessary for proper identification of ZNG and NZNG. In this study, a nontargeted metabolomics approach based on ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) was used to find the differential composition between ZNG and NZNG. Using a combination of single-factor and multivariate statistical analyses, seven compounds with significant differences were discovered and identified, one of which was an unreported compound (a glycoside of pyrrolidine alkaloid). These compounds could be used as single biomarkers for receiver operating characteristic (ROC) analysis. In particular, the binary logistic regression result showed that two sets of combinative biomarkers to distinguish ZNG from NZNG with good sensitivity and specificity. Moreover, there was a significant positive correlation between the two combinative biomarkers and the glycoside of pyrrolidine alkaloid. The results of this study provide new ideas on the developments of ZNG identification, authenticity control and against adulteration in the Chinese circulation market.