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The Tibetan alpine meadow ecosystem is an important part of the Eurasian grasslands and is experiencing intense warming at approximately three times the global warming rate and rapid degradation. However, little is known about the effect of warming and degradation and their interactions on ecosystem functions like soil carbon (C) and nitrogen (N) pools and methane (CH4) uptake in this region. Here, we selected a long-term simulated warming site in a Tibetan alpine meadow with different degradation levels. After 4 years of warming, we analyzed soil total C (TC) and total N (TN) contents, extractable organic C (EOC) and extractable organic N (EON) contents as well as methanotrophic activity, abundance and community structure. Soil EOC and EON contents were measured through hot water extraction, whereas methanotrophic activity was measured along a gradient of CH4 concentrations in laboratory incubations. Michaelis-Menten kinetics analysis [maximal rate of velocity (V-max) and half-saturation constant (K-m)] was used to quantify changes in methanotrophic activity among the treatments. Active methanotrophic communities in the natural soils were measured via DNA-based stable isotope probing (SIP). The results showed that warming significantly increased soil EON contents, whereas degradation significantly decreased soil TC and TN contents, and EOC and EON contents. Methanotrophic activity was significantly lower at different levels of degradation but no significant effects were observed under warming. Changes in soil methanotrophic abundance among the treatments followed the same trend, but warming and degradation had no interactive effects on methanotrophic activity and abundance. Active methanotrophic communities in the natural meadow soils were dominated by Merhylosinus (a Type II methanotroph). In conclusion, our results indicate that soil C and N pools and CH4 oxidation capability were influenced more strongly by degradation than warming. However, warming may have an additional effect on the stability of these important ecosystem processes, regardless of degradation in this region.