Kuroshio and Oyashio Extension (KOE) region is a biological hotspot for carbon cycling and acts as one of the major net sinks for the atmospheric carbon dioxide. Methane is also an important greenhouse gas, while the cycling of methane in the KOE region remains largely unconstrained. Combining high-resolution underway observation, water column biogeochemical analysis and methanotrophic activity measurements, we found a remarkable influence of physical process on the distribution, production and consumption of methane in the KOE region. Water mass mixing not only led to a differentiation in methane concentrations but also drive the shift of phytoplankton and bacterial community. The change of microbial community further influenced the release of methyl-compounds such as DMSP, a potential precursor of methane, as well as aerobic production of methane through the C-P cleavage pathway. Methanotrophic activity was also impacted by the mixing of water mass. In the KOE, aerobic oxidation of methane could account for up to 97% of methane loss, indicating that aerobic methanotrophy significantly reduced methane emission to the atmosphere. Our results suggested that the coupling of physical and biogeochemical processes exerts a significant influence on the cycling of greenhouse gases, providing insights into methane emission in the carbon sink region of the North Pacific Ocean.