The Northeastern part of the South China Sea (SCS) is rich in methane and there is methane seepage on the seafloor. Six sediment cores recovered from the northeastern SCS show that both sulfate and methane contents decrease with depth in the consuming zone of sulfate and methane. Headspace methane of these cores increases with depth and reaches an anomalous high at the bottom of cores. Strong methane seepage will intensify the co-consumption of sulfate and methane, leading to the shift of SMI depths towards the seafloor. The shallow SMIs, which often occur in gas hydrate localities worldwide, imply that the northeastern SCS is a good gas hydrate-prone setting.