Warming and altered precipitation frequently co-occur and jointly influence key carbon cycling processes in alpine ecosystems. However, the interactive effects of these two global change factors on ecosystem respiration (Re) and methane (CH₄) fluxes remain unclear. To address this gap, a long-term field experiment was conducted in an alpine meadow on the Qinghai-Tibet Plateau, combining warming (+2°C) and increased precipitation (+20%). Warming significantly reduced Re by 14.2%, concurrent with a shift from fungal to bacterial dominance. In contrast, increased precipitation enhanced Re by 34.1%, driven by improved soil moisture and greater plant carbon inputs. CH₄ uptake increased under warming (+31.0%) but decreased under increased precipitation (−26.3%), linked to the change in methane-oxidizing bacterial communities. Candidatus Methylumidiphilus, Methylococcus, and Methylomagnum were identified as key predictors. Combined warming and increased precipitation enhanced Re while suppressing CH₄ uptake, indicating that future warming-wetting conditions may intensify carbon losses and weaken the carbon sink capacity of alpine meadows. These findings underscore the necessity of integrating microbial ecological responses into ecosystem models to better predict carbon-climate feedbacks under multifactorial global change.