Aerobic methanotrophic bacteria (AMB) are widely present in biological soil crusts (BSCs) and are important methane-oxidizing groups in desert ecosystems. Grazing disturbance can destroy BSCs, but how it affects AMB is unclear. In this study, the AMB in BSCs under no-, moderate- and heavy-grazing intensities and continuous grazing for 10 years were studied using high-throughput sequencing technology and bioinformatics analysis. The results showed that soil total organic carbon (TOC), dissolved organic carbon (DOC), available phosphorus, and leucine aminopeptidase significantly reduced, while nitrate and ammonium nitrogen and β-1,4-acetylglucosaminidase enzyme activities increased, with increasing grazing intensity. The AMB were highly diverse, with an absolute abundance from 2.97 to 4.95 × 105 (in no and heavy grazing treatments, respectively). Grazing disturbance especially influenced the relative abundance of AMB communities at the genus level. Members belonging to Methylocystis, Methylosinus, and Methylobacter were the top three genera and core methanotrophs in AMB communities, and closely related to the stability of AMB community networks under grazing disturbance. AMB community structure were majorly affected by TOC and DOC. We provide novel insights into grazing could change the soil organic matter, which determinates the abundance, diversity and composition of AMB communities in cyanobacteria-dominated BSCs in desert steppes.