Although coastal sediments are major contributors to the production of atmospheric methane, the effects of environmental conditions on methanogenesis and the community of methanogenic archaea are not well understood. Here, we investigated the methanogenesis pathways in nearshore and offshore sediments from the South Yellow Sea (SYS). Moreover, the effects of the supply of methanogenic substrates (H₂/CO₂, acetate, trimethylamine (TMA), and methanol) and temperature on methanogenesis and the community of methanogenic archaea were further determined. Methylotrophic, hydrogenotrophic and acetotrophic methanogenesis were found to be responsible for biogenic methane production in nearshore sediments. In the offshore sediments, methylotrophic methanogenesis was the predominant methanogenic pathway. The changes in methanogenic community structure under different substrate amendments were characterized. Lower diversities were detected in substrate-amended samples with methanogenic activity. Hydrogenotrophic Methanogenium, multitrophic Methanosarcina, methylotrophic Methanococcoide, Methanococcoide or methylotrophic Methanolobus were dominant in H₂/CO₂-, acetate-, TMA- and methanol-amended sediment slurries, respectively. PCoA showed that the methanogen community in H₂/CO₂ and acetate amendments exhibited greater differences than those in other treatments. Lower temperature (10 °C) limits hydrogenotrophic and acetoclastic methanogenesis, but methylotrophic methanogenesis is much less affected. The response of methanogen diversity to the incubation temperature varied among the different substrate-amended slurries. The multitrophic methanogen Methanosarcina became increasingly abundant in H₂/CO₂₋ and acetate-amended sediment slurries when the temperature increased from 10 to 30 °C.