Aerobic methane (CH₄) oxidation plays a significant role in marine CH₄ consumption. Temperature changes resulting from, for example, global warming, have been suggested to be able to influence methanotrophic communities and their CH₄ oxidation capacity. However, exact knowledge regarding temperature controls on marine aerobic methane oxidation is still missing. In this study, CH₄ consumption and the methanotrophic community structure were investigated by incubating sediments from shallow (Bohai Bay) and deep marine environments (East China Sea) at 4, 15, and 28 °C for up to 250 days. The results show that the abundance of the methanotrophic population, dominated by the family Methylococcaceae (type I methanotrophs), was significantly elevated after all incubations and that aerobic methane oxidation for both areas had a strong temperature sensitivity. A positive correlation between the CH₄ oxidation rate and temperature was witnessed in the Bohai Bay incubations, whereas for the East China Sea incubations, the optimum temperature was 15 °C. The systematic variations of pmoA OTUs between the Bohai Bay and East China Sea incubations indicated that the exact behaviors of CH₄ oxidation rates with temperature are related to the different methanotrophic community structures in shallow and deep seas. These results are of great significance for quantitatively evaluating the biodegradability of CH₄ in different marine environments.