Abstract: Three important geological elements, i.e. high sedimentation rate, strong tectonic activity and high heat flow, promote the wide distribution of hydrocarbon fluid seeps and leakage structures such as mud volcanos and gas chimneys on the western slope of Okinawa Trough. Several previous studies have been conducted to reveal the mud volcano geomorphology and forming conditions, in particular the bottom simulation reflectors of gas hydrate accumulated in the mud volcano. However, rare researches focused on the geochemistry of the pore fluids and the origin of methane saturated in the pore water of sediments recovered from the mud volcano. In this work, seafloor drilling rig was deployed for two shallow holes to recover sediment and pore water samples from the mud volcanos. Geochemical analysis of pore water molecular ratios and isotopic compositions show that C₁/C₂ vary from 960.53 to 1 120.75 in the core 18-01 and from 1 064.66 to 1 546.74 in the core 18-05, while the carbon isotopic values of pore water methane exhibit a variation from −36.07‰ to −56.60‰ V-PDB in the core 18-01 and from −36.10‰ to −62.92‰ V-PDB in the core 18-05 respectively. Combined with molecular ratios, stable carbon and hydrogen isotopic compositions, we conclude that the pore water methane is derived from thermal degradation of organic matter. As the result of conversion from smectite to illite induced overpressure in deep sediments, thermogenic methane was driven along gas chimney and tectonic conduits and migrated to the shallow sediments, then formed mud volcanos and associated methane plumes in the overlying water.