The role of guest−guest and guest−host interactions has been studied in the case of butane-based hydrates. It has been shown that these interactions are different for n-butane and iso-butane isomers. First-principles calculations reveal the weaker interaction of the linear trans-n-butane molecules with the water framework and the contribution of guest−guest repulsive interactions. The strongest interaction is found for the iso-butane hydrate and depends on both host−guest and guest−guest interactions. Calculations of the thermodynamic properties are in agreement with available experimental data. It is shown that the pure trans-n-butane hydrate is thermodynamically unstable. Moreover, the thermodynamic stability can be controlled by adding methane, which can occupy small cavities. The experimental observation of binary n-butane + methane hydrate is confirmed by stabilization of the gauche isomer in large cavities. This indicates the importance of accurate evaluation of weak intermolecular interactions for prediction of the phase diagram and the amount of guest storage.