Increasing evidence shows that warming is driving Hg release from the cryosphere. However, Hg cycling in thawing permafrost is less understood to date. Here we show that permafrost thaw dominantly supplied no-run thermokarst ponds by permafrost melt waters (PMWs) with high concentration of photoreducible Hg (PRHg) and subsequently controlled Hg(0) emissions in the Tibetan Plateau. This study was motivated by field survey suggesting that thermokarst ponds as recipient aquatic systems of PMWs could be an active converter of PRHg to Hg(0). Annual Hg mass balance in three seasonally ice-covered thermokarst ponds suggests that PMWs were the dominant input (81.2% to 91.2%) of PRHg in all three thermokarst ponds, and PRHg input would be a constraint of Hg(0) emission owing to the fast photoreduction of PRHg to Hg(0) in the water column. Annual Hg(0) emission in the thermokarst ponds of study region was conservatively estimated to increase by 15% over the past half century. Our findings highlight that climate-induced landscape disturbances and changes in hydrogeochemical processes in climate-sensitive permafrost will quickly and in situ drive Hg stored in permafrost for a very long time into the modern day Hg cycle, which potentially offsets the anthropogenic Hg mitigation policies.