Clathrate hydrate is a kind of environment-friendly material for storing hydrogen under a certain condition of temperature and pressure. In this work, tetrahydrofuran aqueous solution with concentration of 3.0 mol% was adopted to investigate hydrogen storage process. Moreover, thermal property of hydrate was measured by high pressure differential scanning calorimeter, and mechanism of hydrate-based hydrogen storage was studied by in situ Raman. Especially, gas uptake, morphology and structures change of compounds from gas/liquid interface towards hydrate layer were monitored in the process of hydrate formation. Thermal experiments illustrate that thermal data for tetrahydrofuran-hydrogen binary hydrate under extra high pressures could be effectively obtained by high pressure differential scanning calorimeter, moreover, memory effect shows no influence on thermal state of hydrate but weakly affects water aggregation. Kinetics and microscopic experiments illustrate that a special pressure drop and some tetrahydrofuran hydrates with unstable structure can be found under conditions of 273.15 K and 14.53 MPa. The pressure drop involves into hydrogen molecules tunneling movement among hydrate cavities. Moreover, hydrogen molecules show a positive effect on binary hydrate stability. Further, the density of 1.875 g/Lwater shows that hydrogen storage process via clathrate hydrate is an excellent method to store hydrogen.