Phenolic ingredients of Hippophae tibetana (Tib) and H. rhamnoides ssp. sinensis (Rha) berry from Qinghai-Tibet Plateau were identified by Ultra Performance Liquid Chromatography-triple Quadrupole Tandem Mass Spectrometry. Results demonstrated that both of them possessed high levels of total phenolic and flavonoid, and compared to Tib, Rha berry exhibited higher contents. Moreover, flavonols was the most predominant subclass in Rha berry, flavonols and flavanols were the two most abundant subclasses in Tib berry. Among them, rutin and narcissin were present in the most abundant amounts in Rha berry, while (-)-epigallocatechin was the richest substance in Tib berry. Furthermore, both phenolic extracts of sea buckthorn berry exhibited strong in vitro and cellular antioxidant properties. Rha berry extract exhibited much stronger effects because of its higher levels of phenolic and flavonoid profiles. This finding proved that the Rha berry could serve as a food source for better health with great potential antioxidant activity.