To systematically quantify the production, consumption and migration of methane along a continental margin, 210 sediment cores were collected from offshore southwestern Taiwan and analyzed for their gas and aqueous geochemistry. These data, combined with published results, were used to calculate the diffusive methane fluxes across different geochemical transitions and to develop scenarios of mass balance to constrain deep microbial and thermogenic methane production rates within the accretionary prism. The results showed that methane diffusive fluxes ranged from 2.71 × 10−3 to 2.78 × 10−1 and from ‒1.88 × 10−1 to 3.97 mmol m−2 d−1 at the sulfate-methane-transition-zone (SMTZ) and sediment-seawater interfaces, respectively. High methane fluxes tend to be associated with structural features, suggesting a strong structural control on the methane transport. A significant portion of ascending methane (>50%) is consumed by anaerobic oxidation of methane at the SMTZ at most sites, indicating effective biological filtration. Gas compositions and isotopes revealed a transition from the predominance of microbial methane in the passive margin to thermogenic methane at the upper slope of the active margin and onshore mud volcanoes. Methane production and consumption at shallow depths were nearly offset with a small fraction of residual methane discharged into seawater. The flux imbalance arose primarily due to the larger production of methane through deep microbial and thermogenic processes at a magnitude of 1,512 – 43,096 Tg Myr−1 methane and could be likely accounted for by the sequestration of methane into hydrate forms, and clay absorption.