Hydroxyl radicals (·OH) exert a strong impact on the carbon cycle due to their nonselective and highly oxidizing nature. Reduced iron-containing clay minerals (RIC) are one of the major contributors to the formation of ·OH in dark environments, but their interactions with humic acids (HA) are poorly known. Here, we investigate the mutual interactions between RIC and HA under dark and oxygenated conditions. HA decreased the oxidation rate of structural Fe(II) in RIC but significantly promoted the ·OH yield. HA dissolved a fraction of Fe(II) from RIC to form an aqueous Fe(II)-HA complex. ·OH were generated through both heterogeneous (through oxidation of structural Fe(II)) and homogeneous pathways (through oxidation of aqueous Fe(II)-HA species). RIC-mediated ·OH production by providing H2O2 to react with Fe(II)-HA and electrons to regenerate Fe(II)-HA. This highly efficient homogeneous pathway was responsible for increased ·OH yield. Abundant ·OH significantly decreased the molecular size, bleached chromophores, and increased the oxygen-containing functional groups of HA. These molecular changes of HA resembled photochemical transformation of HA. The mutual interaction between RIC and HA in dark and redox-fluctuating environments provides a new pathway for fast turnover of recalcitrant organic matters in clay- and HA-rich ecosystems such as tropical forest soils and tidal marsh sediments.