Microbial methane (CH4) oxidation is a major global sink of CH4. Aerobic CH4-oxidizing bacteria (methanotrophs) represent a biological model system for CH4 consumption and is very sensitive to climate warming, but still poorly understood. Here we used DNA stable-isotope probing (SIP) coupled with high-throughput sequencing of 13C-DNA to compare active methanotrophs incubated at 10, 15, 20, and 25 °C in 13CH4-fed microcosms from two geographically distinct natural wetlands: Sanjiang Plain wetland in northeast China and Haibei wetland in Tibet Plateau. In both wetlands, CH4 oxidation potential was enhanced with increasing temperature. Community profiling revealed that type I methanotrophs dominated CH4 oxidation, although a small portion (2.76%–17.14%) of type II methanotrophs (Methylocystis, Methylosinus/Methylocystis) were significantly stimulated at 20 °C and 25 °C. 13C-labeled indicator species included Methylobacter, Methylocystis, and Methylosarcina species in Sanjiang Plain, and Methylobacter and Methylosarcina species in Haibei. Network analysis demonstrated positive co-occurrence of species between genera of Methylobacter, Methylosarcina, and Methylocystis with shifts in temperature, while interspecies interactions between Methylobacter and Methylomonas correlated negatively, and Methylobacter and Methylosinus/Methylocystis positively. Partial least squares path modeling illustrated that the direct effects of temperature on CH4 oxidation were stronger in northeast China than Tibet Plateau, and temperature could also indirectly influence CH4 oxidation via shifts in the methanotroph communities. Collectively, these results provide insights into how temperature could influence methanotrophy in natural wetlands under future climate scenarios.