Methane oxidation driven by aerobic methanotrophs plays a critical role in the alleviation of global warming. Yet, we still know little about the assembly mechanisms of methanotrophic communities and the corresponding drivers in mountain soils. Here, we comprehensively investigated methanotrophic bacteria along an elevational gradient (1800–4100 m) in Mount Gongga, China. Our results indicated that previously unrecognized AOB-rel methanotrophs predominated in mountain forest soils, and they showed distinct phylogenetic differentiation and pH preferences (pH 5.9–7.2 and pH 4.7–5.6 for AOB-rel subclade 1 and 2, respectively). Soil pH, temperature and precipitation primarily shaped methanotrophic communities. The community assembly of aerobic methanotrophs was governed mainly by deterministic processes. Our findings also implied that more acidic soils contained less phylogenetically clustered methanotrophic communities, and more neutral soils harbored more phylogenetically clustered communities. This study is the first to illustrate the significant role of soil pH in the assembly of aerobic methanotrophic communities and reinforce the importance of AOB-rel methanotrophs in atmospheric methane oxidation process in mountain forest soils.