Lycium chinense has been used as a traditional medicine for centuries in Asia because of its positive effects on health. However, its functional components have not been elucidated. This study determines the levels of health-promoting lipophilic compounds, including carotenoids, tocopherols, and phytosterol, and those of 42 hydrophilic metabolites, including sugars, organic acids, alcohols, amines, and amino acids, in L. chinense fruit from 11 cultivars. The metabolite profiles were subjected to a principal component analysis (PCA), Pearson correlation analysis, and hierarchical clustering analysis (HCA). PCA showed the Cheongdang (LM-3) cultivar to be distinct from the others. The correlation results for a total of 55 compounds revealed strong correlations between the metabolites that participated on closely related pathways. The Cheongdang cultivar appears to be most suited for functional food production because of its high carotenoid, tocopherol, and phytosterol levels. These results indicate the usefulness of metabolite profiling as a tool for assessing the quality of food.