Atraphaxis pyrifolia, a native medicinal plant of Central Asia, has a long history of traditional medicinal use; however, scientific research on its phytochemical and biological properties remains scarce. This paper aims to elucidate its chemical profile and assess its pharmacological potential through a comprehensive investigation of the phytochemical composition of stems and leaves using Liquid Chromatography-Mass Spectrometry (LC-MS), in conjunction with the assessment of its antioxidant (DPPH and ABTS) and cytotoxicity test on Artemia salina. Predominantly, glycosylated flavonoids were detected in stems and leaves extracts, notably including 8-Acetoxy-3′,4′,5,5′-tetrahydroxy-7-methoxy-3-α-L-rhamno-pyranosyloxyflavone, pyrifolin, and dehydroxypyrifolin. While the latter compound is exclusive to A. pyrifolia, the former compounds serve as shared chemical markers with other Atraphaxis species. The methanolic extracts of A. pyrifolia leaves exhibited significant antioxidant capacity without toxicity against Artemia salina. This study contributes to current research through providing valuable insights into the chemical diversity and potential medicinal properties of this plant species.