We studied the formation micro-mechanism of the small and large cages in the nucleation pathway of 51 methane hydrate using ab initio calculations. We found that the cage precursor is a pentagonal ring of water molecules plus one methane molecule, which is formed through the attraction of the pentagonal water ring to the methane molecule. Due to the difference of the hydrophobic-hydrophilic effects, the ring expansion mechanism and the layer-separated mechanism are observed for the growth of water faces in the small and large cages, respectively. Further, formation of the small cage is more structurally feasible and will locally prefer in the early stage of nucleation, but the large cages will dominate in the crystalline structure of methane hydrate, attributing to their high stabilization energy. (C) 2016 Elsevier Ltd. All rights reserved.