Glacier-fed streams (GFS) are emergent sources of greenhouse gas methane, and methanogenic archaea in sediments contribute largely to stream methane emissions. However, little is known about the methanogenic communities in GFS sediments and their key environmental driving factors. This study analyzed stream sediments from the Rongbuk River basin on Mount Everest for methanogenic communities and their temperature responses through anaerobic microcosm incubations at 5 and 15 degree. Diverse methanogens were identified, including acetoclastic, hydrogenotrophic, and methylotrophic types. Substantial methane and CO2 production were detected across altitudes and increased significantly at 15 degree, with both methane and CO2 production rate negatively correlated with altitude. While temperature sensitivity of CO2 production but not CH4 showed a negative altitude correlation. Methanogens increased substantially over long-term incubation, dominating the archaeal community. At 15 degree, the relative abundance of several methanogenic groups was strongly correlated with altitude, with positive correlations observed for Methanomassiliicoccaceae and Methanoregulaceae, and negative correlations for Methanocellaceae and Methanotrichaceae, respectively. Besides altitude, factors like phosphorus, C-to-N ratio, and pH also affected methanogenic structure, methane and CO2 production, and temperature sensitivities. This study offers new insights into methanogens and methane production in GFS sediments, improving our understanding of GFS carbon cycling and its potential responses to climate change.