Subcritical water extraction and molecular dynamics simulation were performed to investigate mangiferin and antioxidant extraction from Mahkota Dewa fruits at different operating temperatures. The mangiferin yield and antioxidant activity were analyzed using high-performance liquid chromatography and 2-diphenyl-1-picrylhydrazyl assay method, respectively. The diffusivity and intermolecular interactions were determined by mean squared displacement (MSD) and radial distribution function (RDF) analysis, respectively. The temperature exerts a momentous effect on mangiferin yield and antioxidant activity of the extract. The MSD result showed an increment in diffusivity coefficient of mangiferin with temperature. The RDF analysis revealed hydrogen bonding formations between mangiferin and water through O H2O..H MR4(OH1) interaction that plays a role in the extraction process.