Coastal wetlands are critical in global carbon sequestration, but their biogeochemical cycling is highly sensitive to sediment mixing. Here, we quantified the impacts of storm-induced mixing on organic carbon (OC) storage across China's coastal wetlands using multiple radionuclides and machine learning (SHAP model). Field observations and SHAP results identified the storm surge as a key driver of sediment mixing, whose impact weakens with increasing offshore distance and vegetation cover. The vegetated, supratidal site in the Yellow River estuary wetland was less affected by the storm surge with a sediment mixing depth of only 18 cm. Sediment mixing was observed at 80% of stations from the literature in China's coastal wetlands, mainly driven by river discharge and waves. Furthermore, a negative correlation between sediment mixing depth and soil organic carbon (SOC) density (r = −0.42) in the top meter was found. For regions with SOC density > 5 kg m⁻², the depths of sediment mixing are lower than 40 cm. Under the medium-forcing scenario SSP2-4.5 and the high-forcing scenario SSP5-8.5, the average sediment mixing depth in China's coastal wetlands is expected to increase by 19% and 28% by 2100, leading to corresponding declines in SOC density of 2.5% and 3.5%. The findings show that intensified sediment mixing caused by climate warming will weaken the carbon storage capacity of coastal wetlands, providing a crucial scientific basis for the sustainable management of coastal wetlands and the formulation of carbon sink enhancement strategies.