As endangered rare plants, yellow camellia species are narrowly distributed in Guangxi province in Southern China and Northern Vietnam. Apart from being a shining star in horticultural and agricultural field with remarkable commercial and ornamental value, yellow camellias are also widely consumed as popular beverages (tea) worldwide. In this study, for the first time, the phytochemical profiles of the most widely used three yellow camellia species in the current market including Camellia chrysantha (Hu) Tuyama var. phaeopubisperma S. Y. Liang et Z. H. Tang (CC), Camellia euphlebia Merr. ex Sealy (CE), and Camellia insularis (CI) were revealed using an integrated approach based on quadrupole time-of- flight mass spectrometry (UPLC-QTOF-MS/MS) combined with untargeted metabolomics and their anti-oxidant/ anti-inflammatory activities were also determined firstly on RAW264.7 cells. Firstly, 56 predominant constituents in three yellow camellias were rapidly identified by a novel UPLC-QTOF/MS-based strategy and quantitative analysis of 7 common compounds suggested a significant difference of distribution of (-)-epicatechin, procyanidin B3 and astilbin in three yellow camellias. Afterwards, a reasonable method for discrimination of three yellow camellia species was successfully established by untargeted metabolomics and pattern recognition analysis, which achieved a perfectly clear separation of the three yellow camellias. Subsequently, a total of 16 valuable variables for discrimination of three yellow camellias were identified as marker compounds and heatmap visualization was applied for clarifying the distribution of 16 marker compounds in three yellow camellias. Eventually, a noticeable difference of anti-oxidant/ anti-inflammatory capacity on RAW264.7 cells was observed in three yellow camellias. The results indicated CC, CE and CI as functional food resources varied largely both in chemical constituents and anti-oxidant/ anti-inflammatory activity and CE or CI may not be used as the substitution of CC. This study provided a classical example of phytochemical profiling, bioactivity evaluation and discrimination of herbal medicine, functional plant and popular beverage with multiple botanical origins as well as inspiring perspectives for quality evaluation of Chinese medicine.