Harvesting energy gases in the nanoporous water-frameworks of clathrate hydrate enables the widespread of hydrogen-based fuels converted from excess solar or wind energy sources (i.e., Power-to-Gas). However, there has always been a critical trade-off between mild formation condition and maximum working capacity. Here we demonstrate the ‘natural gas modulator’ based synthesis that leads to significantly reduced synthesis pressure (≈3 MPa) simultaneously with the formation of hydrogen clusters (up to 3 molecules) in the confined nanoporous cages of clathrate hydrates. Instead of employing hazardous liquid chemicals, clean energy gas of natural gas is used for the first time to multiply load H2 in all cages (512, 51262, and 51264 cages) of hydrogen-natural gas hydrates without any postsynthetic modification (e.g., guest-exchange reaction). This approach minimizes the environmental impact and reduces operation cost since clathrate hydrates do not generate any chemical waste in both synthesis and decomposition process, and hydrogen-natural gas mixture can be also utilized as an energy resource as itself.