Distinct morphological MgO nanoparticles (MgONPs) were synthesized using biomasses of Saussurea costus roots. The biomass of two varieties of Saussurea costus (Qustal hindi and Qustal bahri) were used in the green synthesis of MgONPs. The physical and chemical features of nanoparticles were confirmed by spectroscopic and microscopic techniques. The surface morphology of the obtained nanoparticles was detected at different magnifications by SEM and TEM microscopy and the size of nanoparticles were found to be 30 and 34 nm for Qustal hindi and Qustal bahri, respectively. The antimicrobial activity of the prepared MgONPs was screened against six pathogenic strains. The synthesized nanoparticles by Qustal bahri biomass exerted significant inhibition zones 15, 16, 18, 17, 14, and 10 mm against E. coli, P. aeruginosa, C. tropicalis and C. glabrata, S. aureus and B. subtilis as compared to those from Qustal hindi 12, 8 and 17 mm against B. subtilis, E. coli and C. tropicalis, respectively. MgONPs showed a potential cytotoxicity effect against MCF-7 breast cancer cell lines. Cellular investigations of MgONPs revealed that the prepared nanoparticles by Qustal bahri exhibited high cytotoxicity against MCF-7 cancer cell lines. IC50 values in MCF-7 cells were found to be 67.3% and 52.1% for MgONPs of Saussurea costus biomasses, respectively. Also, the photocatalytic activity of MgONPs of each Saussurea costus variety was comparatively studied. They exhibited an enhanced photocatalytic degradation of methylene blue after UV irradiation for 1 h as 92% and 59% for those prepared by Qustal bahri and Qustal hindi, respectively. Outcome of results revealed that the biosynthesized MgONPs showed promising biomedical potentials.