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Methane seeps are widespread at continental margins, and may exert an influence on climate change. However, many details concerning the relationship between methane seepage and climate change in the geological history remain unclear. Geological records of cold seeps at glacial‐interglacial transitions remain scarce due to the lack of relatively complete records. Here we present geochemical data of seep carbonates from a drill core from the South China Sea, which reveals three stages of methane seepage linked to the dissociation of biogenic methane hydrate: ∼130.3 ka BP before, MIS 5 (∼130.3 to 111.4 ka BP) and MIS 1 (∼11.1 to 10.0 ka BP). Our results evidence that methane seepage was induced by warm seawater and subsequently hydrostatic pressure drop during deglaciations. We suspect this process to occur in other world regions and infer that methane seepage might occur more widespread at glacial‐interglacial transitions, which in turn might have accelerated global warming.