Aim: The aim of the study was Identification and quantification of phenolic compounds, total flavonoides content and antioxidant potential of flower buds, foliages, bark and root of a perennial herb, Calligonum polygonoides (Phog) of Thar Desert. Methodology: The methanolic extracts of different plant parts of C. polygonoides were subjected to LC-MS/MS (Waters Acquity UPLC-PDA, TQD) analysis for phenolic identification and spectrophotometric assay of total phenolic and flavonoids content and total antioxidant activity was estimated. Results: A total of 15 phenolic compounds were identified and quantified, among which gallic acid content was abundant, followed by catechin. Besides these, the other major phenolic compounds detected in different plant parts were vanillic, chlorogenic acid, epicatechin, coumeric acid, catechol, vanillic acid, epicatechin and syringic acid. Extremely higher values were recorded for total phenolics, flavonoids and antioxidant capacity. The values for phenol, flavonoids and total antioxidant activity in bark extracts were higher than that of clove extract. Interpretation: The identified phenolic compounds possess high antioxidant potential. These results provide scientific evidence for use of C. polygonoides as safe natural antioxidant compounds in nutraceutical and pharmaceutical industry.