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Warming greatly reshapes carbon cycle of peatlands where soil is water saturated with anaerobic condition prevailing all the year round. However, little is known about the response of anaerobic mineralization of peatlands carbon to global warming, especially when considering the difference of soil from above water table (AWT) and below water table (BWT). This study measured variations in soil carbon anaerobic mineralization as a function of warming and depth by sampling 100-cm soil columns in Zoige plateau. Warming enhanced carbon anaerobic mineralization significantly with different increments among the whole depths. The response of CO2-C and CH4-C to warming varied with depth: at surface soil, both CO2-C and CH4-C emission increased with higher increment; at deep soil, CO2-C emission increased with small increment and CH4-C emission decreased. Substrate availability influenced carbon anaerobic mineralization rate and pathway. Substantial resistant carbon at deep soil lowered CO2 increment and varied CH4 production pathway. The temperature sensitivity of peat carbon anaerobic mineralization varied with depth, suggesting the heterogeneous distribution of soil substrate among the whole depths. AWT soil was higher in temperature sensitivity than BWT soil for the substantial simple carbon and higher microbial/enzyme activity at AWT. BWT soil was a major contributor of the amount of carbon emission and the total increased carbon caused by warming. Further, for the management of peatlands, we should conduct advanced research by focusing more towards the soil of whole depth, especially on the temperature sensitivity of AWT soil and the contribution to total carbon emission of BWT soil.