Multidrug resistance is an instance of the increased use of traditional drug therapy, which includes the consumption of antibiotics and anticancer drugs. It will take alternative treatments to overcome this obstacle. Nanoparticles that are biosynthesized are extensively used to address a range of illnesses. This study aims to investigate the aqueous extracts of Cyperus rotundus used to biosynthesis hybrid nanoparticles using magnesium (Mg) and palladium (Pd) nanoparticles (NPs). Herein, different characterization techniques are used to the reveal desired physiochemical properties and potential biomedical applications of the biosynthesized NPs. With the use of centre composite design (CCD), the most significant parameters and their interactions that are likely to affect nanoparticle synthesis were assessed and identified in order to improve the quality of the experiments. The Mg/Pd NPs exhibit exerting antimicrobial activity against Gram positive and Gram negative bacterial and fungal pathogens. Significant anticancer activity was observed in the biogenic hybrid NPs against the human hepatocellular carcinoma (HuH-7) cell line. In silico molecular docking studies confirmed strong binding interactions of D-Glucose cyclic 1, 2-ethandiylmercaptal pentaacetate compound with the HuH-7 cancer cell line, as well as with EGFR tyrosine kinase inhibitor resistance and Bcl2 gene target proteins. The findings also point to intriguing possibilities for incorporating C. rotundus extract-assisted hybrid nano-biosynthesis, which is crucial for developing cutting-edge nanomedicines.