Peatlands are a major natural source of atmospheric methane (CH₄). Yet their responses to warming remain highly uncertain, because ecosystem-level understanding of warming effects on CH₄ production and oxidation is limited. Here, we conducted an open-top chamber (OTC) warming experiment in the world's largest alpine peatlands (Zoige) under both waterlogged and drained regimes. We monitored stable carbon isotopic composition (δ¹³C) of CH₄ and CO₂ in soil gas and porewater throughout five growing seasons, coupled with net CH₄ fluxes, to tease apart OTC warming effects on methanogenesis (quantified as in situ CH₄ production, PCH₄) and methanotrophy (quantified as the fraction of CH₄ oxidized during upward diffusion, fox). Warming did not alter net CH₄ fluxes from the waterlogged regime, because PCH₄ and f_ox declined concurrently owing to enhanced iron reduction and elevated reducing conditions, respectively. In contrast, OTC warming reduced net CH₄ fluxes by ~60% from the drained regime, mainly because methanotrophy intensified (mean f_ox increased by 41%) due to increased oxygen availability and reduced aerenchymatous plant biomass. The decline in aerenchymatous plants limited plant-mediated transport and bypass of CH₄ across the oxic soil layer. Enhanced methanotrophy was further supported by increased soil abundance of methanotroph-specific phospholipid fatty acid markers. Collectively, our results reveal contrasting responses of CH₄ emission to OTC warming in waterlogged versus drained alpine peatlands and identify vegetation composition as a key determinant of peatland CH₄ trajectories under warming. These findings highlight hydrological status and vegetation composition as key controls over ecosystem-level responses of peatland CH₄ production and oxidation to warming and emphasize the need to represent these controls explicitly in projections of peatland CH₄ dynamics.