Hydrothermal systems are ubiquitous in various tectonic settings and are important in transferring internal mass and energy sources from the crust and mantle to the oceans. However, the biogeochemical processes involved in subseafloor hydrothermal circulation are not fully understood. This study investigated the compositional and isotopic properties of the high-temperature fluids collected from three hydrothermal vents of the Izena Hole in the middle Okinawa Trough in 2016 with Remotely Operated Vehicle (ROV) named Faxian. The results confirm that the latest geochemical parameters of the high-temperature hydrothermal fluids are similar to the previously reported parameters and indicate the origin of methane in the hydrothermal fluid. The nearly identical geochemistry of the three fluids indicate that they likely shared a common fluid reservoir. The endmember hydrothermal fluid contained isotopically 13C-moderate methane (− 30.4‰ to − 32.1‰), suggesting the predominance of thermogenic methane over biogenic methane incorporation in the hydrothermal fluids. The differences in the concentrations of ethane (C1/C2+ = 11,600, 5600, 970 for Faxian-1, Faxian-2, and Faxian-3, respectively) and molecular hydrogen (0.11, 0.67, and 2.4 mM for Faxian-1, Faxian-2, and Faxian-3, respectively) suggest significantly different thermal fluid-sediment interaction during the discharge stage between two hydrothermal fields. The relatively low contents of biogenic methane in all the fluids here indicated limited biogenic methane incorporation during the recharge stage due to the horizontal restriction of hydrothermal fluid circulation. The geochemical origins of methane in hydrothermal fluid and their relevance to hydrothermal fluid circulation revealed herein shed light on the different degrees of sediment influence in various geological/geographical settings in the Okinawa Trough.