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Sediments on continental slopes, which are rich in hydrates and organic matters, may release methane into the overlying seawater and even into the atmosphere. To evaluate the impact of sediment emissions on oceanic methane cycling and greenhouse gas emissions, this study assessed the distribution of methane in surface sediments and water columns and calculated the sea-to-air methane flux in the Dongsha area of the northern South China Sea. Results show that the methane concentrations exhibited large spatio-temporal changes. In May 2019, the methane concentrations and sea-to-air methane flux (4.1 ± 3.7 μmol m−2 d−1) were close to the background values, indicating that in situ aerobic methane production was a weak atmospheric methane source. In contrast, in September 2020, abnormally high methane concentrations up to 26.6 nM were detected in the upper slope with water depths of 600–950 m and to the east of a seamount; the average sea-to-air methane flux increased to 11.3 ± 7.9 μmol m−2 d−1. The consistency of methane distribution throughout the water column and surface sediments, with a generally increasing trend with the increasing depth, indicates that in September 2020, sediment emissions were crucial methane sources in seawater and led to moderate emissions into the atmosphere. The heterogeneities of methane concentrations and sea-to-air methane fluxes were attributed to the uneven distribution of methane in the sediments. Besides, strong internal solitary waves in summer and autumn exacerbates methane release, especially around high terrain areas, such as in continental upper slopes and in the upstream side of seamounts. Our results demonstrate that methane released from the sediments, being perhaps affected by internal solitary waves induced sediments disturbance, substantially impacted the oceanic methane cycling in continental slopes. Thus, this study provides new insights into the methane budget of marginal basins. • Abnormally high methane concentrations were detected in the upper slope and to the east of a seamount. • Sediment emissions were crucial methane sources in seawater in the Dongsha area. • ISWs enhance methane released from sediments into atmosphere near high terrain areas in Autumn. [ABSTRACT FROM AUTHOR]