Submarine methane seepages constitute an important part of global carbon cycle and may be promoted by the dissociation of gas hydrate. The migration pattern of a seepage is commonly dominated by vertical transport of methane-rich pore fluids, and then lateral migration of these fluids probably occurred due to self-sealing effect of carbonate crust above vertical migration conduit. Some studies found the evidence of this lateral migration, but the one from the record of seep carbonate in nature is very rare. In this study, we present the results of mineralogical, isotopic, and dating analyses of a core containing seep carbonates obtained from seafloor drilling site D5 in the Middle Okinawa Trough. The core contains 0.98-m-long carbonate interval that predominantly consists of aragonite, with an average content of ∼86.6%. The carbonate exhibits moderate depletion in 13C (δ13C values: −37.2‰ to −16.3‰ Vienna Pee Dee Belemnite; VPDB) and enrichment in 18O (δ18O values: 4.3‰–5.8‰ VPDB), with relatively constant 87Sr/86Sr values (0.709167–0.709197). These results suggest that the precipitation of the seep carbonate was induced by the sulfate-driven anaerobic oxidation of methane close to the seabed and this methane could be from the dissociation of gas hydrates. U–Th age–depth profile shows that two carbonate intervals grew downwards coevally to coalesce into a thicker crust, and its upper segment also grew upwards. We interpret that lateral migration of the fluid flows at two levels are responsible for the formation of upper and lower segments of carbonate intervals because they have (a) the distinct clustering of δ13C and δ18O values and (b) a coeval period of fast growth. It is likely that upward migration of methane was redirected by self-sealing of overlying carbonate crust, leading to lateral migration at the flank of seabed mound Db4 during 6.2–4.6 ka. Our findings highlight the interaction between fluid flows and authigenic carbonates during Late Quaternary, which implies that more methane could be consumed by oxidation because it takes longer time for methane to bypass self-sealing of carbonate to escape into the ocean.