Wetlands provide important ecosystem services, such as water conservation, biodiversity protection, and carbon sequestration. The Zoige alpine wetland is the largest high-altitude swamp in the world and plays a critical role in regional ecological balance and climate change. However, little is known about the fate of its soil organic carbon (SOC) storage. In this study, we estimated the degradation status of the wetland over the past 35 years and used machine learning to investigate the dynamics and driving factors of SOC at different soil depths of the Zoige wetland in 1985, 2000, and 2020. We also simulated the future SOC balance under different scenarios. The results showed that the area of Zoige wetland has degraded by 378.71 km2 in the past 35 years. Increased precipitation and solar radiation offset the adverse effects of global warming, making the soil act as a carbon sink in the past 35 years. The total SOC storage of the wetland soils in 1985, 2000, and 2020 was estimated to be 2.03 Pg, 2.05 Pg, and 2.21 Pg, respectively, with 46.95% of SOC distributed in the subsoil layers. Climate change was the most important driving factor controlling the SOC storage of the Zoige wetland, explaining 51.33% of the SOC changes in the soil. Temperature change was always the most important factor controlling wetland SOC, and precipitation had a greater impact on the topsoil. Under the temperature control targets of 1.5 °C and 2 °C, the SOC pool of the Zoige wetland will decrease by 60.21 Tg C and 69.19 Tg C, respectively. Under scenarios of a 10% and 20% increase in precipitation, the wetland soil will accumulate an additional 46.53 Tg C and 118.89 Tg C, respectively. The study results provide important references for the sustainable management of the Zoige wetland under the background of global climate change.