Understanding processes controlling the atmospheric methane (CH₄) mixing ratio is crucial to predict and mitigate future climate changes in this gas. Despite recent detailed studies of the last  ∼  1000 to 2000 years, the mechanisms that control atmospheric CH₄ still remain unclear, partly because the late Holocene CH₄ budget may be comprised of both natural and anthropogenic emissions. In contrast, the early Holocene was a period when human influence was substantially smaller, allowing us to elucidate more clearly the natural controls under interglacial conditions more clearly. Here we present new high-resolution CH₄ records from Siple Dome, Antarctica, covering from 11.6 to 7.7 thousands of years before 1950 AD (ka). We observe four local CH₄ minima on a roughly 1000-year spacing, which correspond to cool periods in Greenland. We hypothesize that the cooling in Greenland forced the Intertropical Convergence Zone (ITCZ) to migrate southward, reducing rainfall in northern tropical wetlands. The inter-polar difference (IPD) of CH₄ shows a gradual increase from the onset of the Holocene to  ∼  9.5 ka, which implies growth of boreal source strength following the climate warming in the northern extratropics during that period.