This paper reports the thermodynamic and crystallographic properties of the binary clathrate hydrate with methane + 1,1,1,3,3-pentafluoropropane (HFC-245fa) by phase equilibrium measurements, powder X-ray diffraction (PXRD) measurements, and first-principles and thermodynamic calculations. The four-phase (methane gas + water liquid + HFC-245fa liquid + hydrate) equilibrium conditions are lower in pressure by approximately 2−3 MPa than those of the methane + trans-1,3,3,3tetrafluoropropene [HFO-1234ze(E)] hydrates at each temperature from 274.5 to 282.17 K, in spite of the similar molecular structure of HFC-245fa and HFO-1234ze(E). The crystallographic structure of the hydrate with methane + HFC-245fa was identified to be structure II by the PXRD measurement; although because of its molecular length, HFC-245fa would be expected to be encapsulated into a 51268 cage of structure H hydrate. First-principles calculations revealed that these thermodynamic and crystallographic phenomena are the result of two physical factors. First, the total HFC-245fa−water interactions in the cages are stronger than the HFO-1234ze(E)−water interactions due to the presence of more fluorine atoms at the two edge groups in the HFC-245fa molecule and the resulting higher dipole moment of HFC-245fa, and second, the HFC-245fa−HFC-245fa interaction is more greatly enhanced by the presence of methane compared to the HFO-1234ze(E)−HFO-1234ze(E) interactions.