AbstractWe present a systematic model that links the generation, migration, phase partitioning, and accumulation of methane into a closed loop as the sediment is deposited from the seafloor and buried through the base of hydrate stability zone (BHSZ). In our model, methane is generated by biodegradation of organic carbon in muds. Hydrate does not form and methane is not trapped until a coarse‐grained layer is deposited, because the small pores prevent hydrate formation in muds. Instead, methane diffuses into sands/silts where methane solidifies into hydrate. As hydrate‐bearing sands/silts pass through the BHSZ during sediment burial, methane hydrate dissociates, and releases free gas. The released and the newly generated free gas below the BHSZ concentrates into a vertical/dipping zone with low capillary entry pressure and high permeability and flows upward driven its buoyancy. When free gas reaches the hydrate stability zone (HSZ), capillary forces drive free gas to flow laterally, preferentially enter sands/silts, feed hydrate growth, and elevate hydrate saturation. With three‐dimensional focused free gas flow, microbial methane that is generated from a much larger fetch area of the entire basin, both above and below the BHSZ, is concentrated into coarse‐grained layers at structural closures for hydrate formation. Our model illustrates how geological evolution, microbial methane generation, and gas flow by buoyancy couple to generate concentrated hydrate deposits in geological system. These insights can be used to explore for high‐concentration methane hydrate and are important for understanding the methane budget and carbon cycle under the seafloor.