Climate-induced permafrost thaw unlocks large organic carbon stores. Permafrost rivers receive substantial terrestrial inputs of thawing organic carbon (OC) that is mostly degraded to photochemical and microbial respiratory carbon dioxide (CO2). Yet, there is little information on how photochemical and microbial processes combine to alter fluvial carbon dynamics, and ultimately, carbon budget in permafrost areas. Our results from permafrost rivers on the Qinghai-Tibet Plateau mechanistically describe that photodegradation, as a rate limiting and priming step, initiates ring cleavage reactions, rapidly reducing dissolved OC (DOC) molecular weight from aromatic to aliphatic compounds. This in turn resulted in alteration of riverine microbial communities, further converting photo-altered DOC to CO2. Strikingly, the combination of photochemical and microbial processes forms a synergistic interplay, expediting CO2 delivery to the atmosphere, of which 33 ± 10% is derived from millennial-aged permafrost carbon. Our findings highlight that strong solar radiation at high-altitude accelerates microbial CO2 production, and emission, from photo-altered permafrost DOC, contributing to the permafrost carbon feedback that intensifies warming.