As the primary oxidative substance in natural atmospheric wet deposition, hydrogen peroxide (H₂O₂) can undergo in situ Fenton reactions upon introduction into wetland systems. The impact of the resulting generation of powerful oxidative free radicals on the "carbon sink" function of wetlands has been relatively understudied. In this research, indoor simulated experiments were conducted to explore the influence of inputting natural oxidative precipitation of H₂O₂ on soil organic carbon transformation and greenhouse gas emissions in wetlands. The study aimed to reveal the potential effects of in situ Fenton reactions triggered by H₂O₂ on the "carbon sink" function of wetlands. The results indicated that the external input of H₂O₂ significantly promoted the transformation and degradation of soil organic carbon in wetlands. The content of particulate organic carbon (POC), easily oxidizable organic carbon (EOC), and soluble organic carbon (DOC) in the H₂O₂-treated group decreased significantly (P < 0.05), particularly in wetland soils with higher carbon content. Meanwhile, continuous greenhouse gas monitoring over three months revealed that the natural H₂O₂ deposition treatment significantly enhanced the cumulative emissions of CH₄ and N₂O in the wetland system (P < 0.05), while the cumulative emission of CO₂ was slightly higher than that of the control group but not statistically significant (P > 0.05). This suggested that the input of natural oxidative precipitation of H₂O₂ not only plays a promoting role in the transformation of soil organic carbon in wetlands but also triggers the release of greenhouse gases, especially with a more significant increase in CH₄ and N₂O. This process accelerated the decomposition of organic carbon, ultimately producing low-molecular-weight compounds and gas products such as CO₂ and CH₄. In summary, the input of H₂O₂ from natural atmospheric oxidative deposition catalyzed the decomposition of organic carbon in wetland soils, increasing the rate of carbon cycling in the soil and influencing the carbon dynamics of wetland ecosystems. Understanding this process can contribute to a more comprehensive understanding of the mechanisms of soil carbon cycling in wetlands, with significant scientific implications for the management and conservation of wetland ecosystems.