The genus Polygala (Polygalaceae), comprising about 670 species worldwide, has more than 40 species in China. The roots of Polygala tenuifolia Willd., Polygala sibirica L., and Polygala japonica Houtt. are recorded in the Chinese Pharmacopeia. Other closely related plants of the Polygala genus are also widely used in the folk medicine of southern China, such as Polygala fallax Hemsl., Polygala arvensis Willd., and Polygala glomerata Lour. To systematically compare the chemical compositional and elucidate characteristic compounds among the Polygala genus, six Polygala species, namely P. tenuifolia, P. sibirica, P. japonica, P. fallax, P. arvensis and P. glomerata, underwent comprehensive phytochemical studies using the ultra performance liquid chromatography-quadrupole time-of-flight tandem mass Spectrometry (UPLC-Q-TOF-MS/MS) technique, resulting in the identification of 154 compounds, consisting of 62 oligosaccharide esters (40.26 %), 58 saponins (37.66 %), 29 xanthones (18.83 %), and 5 other chemicals (3.25 %). Based on the Masslynx computational tool, a comprehensive comparative phytochemical profiling was achieved and revealed differences in composition among the six Polygala species. P. sibirica exhibited higher levels of specific compounds and was more closely related to P. tenuifolia. Meanwhile, P. japonica showed greater similarity to P. fallax, P. arvensis, and P. glomerata. Oligosaccharide esters and triterpene saponins were more abundant in P. sibirica and P. tenuifolia than in other species. Furthermore, the antioxidant activities (1,1-diphenyl-2-acrylohydrazide [DPPH], 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt [ABTS], copper ion reducing antioxidant capacity [CUPRAC], and ferric ion-reducing antioxidant power [FRAP]) of the six species were evaluated. Among them, P. tenuifolia demonstrated superior antioxidant potential, with a lower half-maximal inhibitory concentration (IC50) value for scavenging DPPH radicals and excellence in CUPRAC (119.85 ± 16.28 μM/0.01 g) compared to other plants. P. japonica showed higher ABTS (98.94 ± 0.03 μM/0.01 g) and FRAP (42.58 ± 0.08 μM/0.01 g). Total flavonoids showed remarkable antioxidant capabilities among the six medicinal plants. Total saponins and phenolics also contributed to the antioxidant potential of these plants. The systematic data and results obtained may provide methodological support for further evaluating the potential use of folk Polygala plants as new effective materials in various commercial sectors, including food, cosmetic, and pharmaceutical industries.