Guest-host hydrogen bonding strongly affects the physical properties of clathrate hydrate, such as the thermodynamic stability, water dynamics, and dielectric properties, but attempts to quantify the effects of hydrogen bonding on these properties are rare thus far. As a preliminary work, this study investigates methane clathrate hydrates with three diazine isomers, pyrazine, pyrimidine, and pyridazine, which expect nearly the same van der Waals volumes due to their similar molecular shapes and sizes, and their guest-host hydrogen-bonding behaviors. The crystal structures of all three binary diazine + CH4 hydrate phases were identified as a cubic Fd (3) over barm structure, including diazine molecules in the 5(12)6(4) cavity, commonly termed as structure II hydrate, by a high-resolution powder diffraction pattern analysis. The phase equilibrium curves of their clathrate hydrates were obtained by the P-T trajectory of the hydrate formation and dissociation process, and the thermodynamic stability trend was well-explained by the guest-host hydrogen bonding behavior as evaluated by the molecular polarities, proton affinities, and ring-breathing vibration frequencies of the three diazine isomers obtained from Raman spectroscopy. This study provides useful information that contributes to the realization of the expansion of the thermodynamics of clathrate hydrates to include guest-host hydrogen-bonding interactions.