In the recent years, significant attentions have been paid to the methane hydrates because of their important role as an energy source. Previous studies reported formation of gas hydrates into carbon nanotubes (CNTs) and between graphene surfaces. In this study, for the first time, we examined the possible formation of methane hydrate containing 8, 10, 12, 14, 16, 18, and 20 water molecules into C240 fullerene using molecular dynamics (MD) simulations. Our results showed that the absorption energy for addition of one methane molecule into confined water molecules is negative. The radial distribution function (RDF) results also indicated that the water and water + methane structures into the fullerene are in the solid state at 300 K. For the systems containing 8–12 water molecules, the methane molecule is out of the ice structure whereas the methane is into the ice cage in the 18 and 20 water structures. After positioning the methane molecule into the fullerene containing 20 water molecules, the confined water molecules created a nearly complete dodecahedron shape and the methane molecule was into the center of the dodecahedron. This is the most ordered polygonal structure of the methane clathrate formed into the C240 fullerene which is more stable than the other clathrate structures and is not formed in C180, C320, and C540 fullerenes. Our DFT computation also approved this ordered polygonal clathrate structure.