1. Climate warming can alter ecosystem carbon (C) balance and also the composition of soil organic matter (SOM), with important local and global implications. However, the extent to which rising temperature affects SOM composition in permafrost ecosystems remains poorly understood. 2. Here, we experimentally warmed a permafrost ecosystem by open-top chambers (OTCs) on the Tibetan Plateau for four years to quantify the responses of C inputs via vegetation production, C losses via soil respiration, and soil organic carbon (SOC) stocks in the top 30 cm. We also characterized the molecular composition of SOM using 13C nuclear magnetic resonance (NMR) and biomarker analyses. 3. The results indicated that warming treatment significantly increased root biomass, soil respiration, heterotrophic respiration and its contribution to soil respiration by 16.7%, 49.0%, 63.2% and 9.5%, respectively. While we observed no change in SOC stocks, warming altered SOM composition in the 0-10 cm layer during the fourth experimental year. Warming increased the abundance of the alkyl C component (3.9%) and decreased aromatic C (5.1%), primarily lignin. The decrease in lignin-derived compounds was attributable to the increased soil phenol oxidase activity. 4. Overall, the substantial increase in heterotrophic respiration and rapid degradation of relatively recalcitrant C components such as lignin demonstrate that Tibetan SOC stocks are vulnerable to climate warming, which could trigger positive C–climate feedback in a warmer world.