Summary Direct conversion of methane to high-value-added chemicals is a major challenge in catalysis, which usually requires high-energy input to overcome the reaction barrier. We report that graphene-confined single Fe atoms can be used as an efficient non-precious catalyst to directly convert methane to C1 oxygenated products at room temperature. A series of graphene-confined 3d transition metals (Mn, Fe, Co, Ni, and Cu) were screened, yet only single Fe atoms could catalyze the methane conversion. Combining in operando time-of-flight mass spectrometry, 13C nuclear magnetic resonance, and density functional theory calculations, we found that methane conversion proceeds on the O–FeN4–O active site along a radical pathway to produce CH3OH and CH3OOH first, and then the generated CH3OH can be further catalyzed to form HOCH2OOH and HCOOH at room temperature.