Gas hydrate plugging in oil and gas transportation pipelines is a knotty problem for flow assurance practices. The nucleation mechanism of methane hydrate on corroded iron pipeline surface is still unclear. In this work, both smooth and corroded iron particles were packed into a hydrate reactor to investigate the relationship between the induction time of methane hydrate and the liquid–metal contact area. Experimental results indicated an insignificant difference among the particles of varied specific surface areas when submerged in the aqueous phase. However, the induction time was reduced by more than 60% when the particles were located above the gas–liquid interface and further shortened by 80% if the particles were corroded. Molecular dynamics simulations indicated that decreased interlayer spacing between the iron layers would facilitate methane hydrate formation in the initial period. Based on our energy analysis, this was ascribed to an increased curvature of the gas–liquid interface, causing a decrease of energy barrier by 54% for a methane molecule to transfer from the interface into the bulk liquid and subsequently, an increase of methane concentration in solution. Meanwhile, two layers of water molecules were observed to adsorb on the iron surface stably and no hydrate cages formed in such region throughout the simulation time. The microscopic phenomenon agreed well with the experimental results, which highlighted the influence of the gas–liquid–metal three-phase interface other than the liquid–metal contact area upon methane hydrate nucleation. The results shed new insights on predicting the prioritized locations of methane hydrate formation in metallic pipelines to reduce the potential hydrate plugging risk.