Equilibrium conditions of methane hydrate formation in the lumens of natural clay nanotubes were analyzed. The water adsorbed by the pristine nanotubes is capable to form methane hydrate in the confined hydrophilic inner pores of 10-100 nm (surface chemistry of the inner lumens is Al2O3, and external tube's surface is SiO2). From 17.5 wt % of water adsorbed by the clay, 12 wt % was involved in methane hydrate formation (conversion ≈ 70%). The crystal structure of the hydrate inside the nanoconfined spaces of halloysite did not change as compared with bulk systems. The formation of methane hydrate occurs during cooling at 0-6 °C simultaneously over the whole clay sample, indicating the catalytic activity of halloysite surface. This formulation slows down decomposition of the hydrate confined in the pores at atmospheric pressure at temperatures below 0 °C. The water is retained in the inner clay pores over the formation and decomposition of methane hydrate. We also modified halloysite nanotubes with mesoporous silica MCM-41 (similar silica gel and sand are routinely used for gas hydrate formation) increasing the ratio of SiO2 to Al2O3 to compare methane hydrate formation in these chemically different pores. This allowed us to decrease substantially pore dimensions in the hybrid system (to 2-3 nm). The fraction of methane hydrate stable within the temperature range from -18 to 10 °C in this smaller pore hybrid system was 8 times less as compared to unmodified halloysite. The very small pores of the halloysite/MCM-41 system allowed formation of hydrate only at a temperatures significantly less than -18 °C. Natural halloysite clay nanotubes were suggested as efficient solid containers for methane hydrates encasing. Halloysite is cheap and scalable up to thousands of tons; it is a mesomaterial capable of methane storage in clathrate hydrates with water-based green chemistry processing. Suggested nanoclay-based hydrate technology is also prospective for gas separation.