Lycii Fructus (Wolfberry Fruit), the fruit of Lycium barbarum or L. chinense is an official Yin strengthening agent in the Pharmacopoeia of Taiwan. It is well known in Chinese herbal medicine for its restorative function of benefiting the liver and kidney, enhancing the immune system, replenishing vital essence, and improving eyesight. Several categories of active metabolites from L. barbarum fruits have been classified, such as polysaccharides, carotenoids, and flavonoids. The composition of the fruit of L. chinense appears similar. To better use the Taiwanese traditional herbal medicine, L. chinense was cultivated as a treasured crop by Miaoli District Agricultural Research and Extension Station, and has been successfully popularized. In our previous study, we reported the value-added development of the aerial parts of L. chinense in Miaoli for food products and dietary supplements. However, very few pharmacognosy and phytochemical studies of Taiwanese L. chinense fruit were reported. The aim of the present study was to establish the standardization of Taiwanese L. chinense fruit. Two different cultivars of L. chinense fruits in Miaoli were prepared and investigated with the microscopic examination, thin-layer chromatography (TLC), as well as high-performance liquid chromatography (HPLC). The data showed that L.chinense fruits had similar histological characteristics but different TLC and HPLC metabolomics profiles when compared with those of L. barbarum.