The climate-active gas isoprene (C5H8) is one of the most abundant biogenic volatile organic compounds (VOCs). Soil is one of the significant sinks for isoprene, yet the role played by the naturally abundant birnessite in the soil surface layer during the oxidation of isoprene remains largely unknown. This study investigates the reactions of isoprene with triclinic and hexagonal birnessite on the Earth's surface environments. Hexagonal birnessite exhibits a superior oxidation capacity than triclinic birnessite, rapidly oxidizing isoprene. The transformation of birnessite from triclinic to hexagonal increases the number of interlayer Mn(III) octahedra, which creates numerous sites for isoprene oxidation. In-situ DRIFTS and DFT calculations indicate that abundant electrophilic active species on the surface of hexagonal birnessite, such as interlayer Mn(III) octahedra and 1O2, oxidize isoprene by attacking conjugated double bonds. Furthermore, birnessite exhibits excellent photoelectric response and photothermal effects, enabling sunlight irradiation under natural conditions to accelerate the oxidation of isoprene by birnessite. The findings of this study elucidates the critical role of birnessite in the oxidation of isoprene and shed light on the fate of isoprene in soil minerals.