CH₄ recovery using CO₂ injection into natural gas hydrates is very attractive because it can perform dual functions of energy production and CO₂ sequestration. In this study, the CH₄-CO₂ replacement that occurs in various gas hydrate structures (sI, sII, and sH) was investigated with a primary focus on phase behavior, structural transformation, and dissociation enthalpy change. To verify the influence of CO₂ injection on the thermodynamic stability of gas hydrates, phase equilibria of the initial CH₄ hydrate (sI), CH₄ + C₃H₈ hydrate (sII), and CH₄ + 2,2-dimethylbutane (neohexane, NH) hydrate (sH) were compared with those of corresponding gas hydrates replaced with CO₂. After the replacement reaction was completed, significant shifts in the hydrate equilibrium curves of each system were observed, which indicates that the substantial extent of the replacement was achievable through CO₂ injection. The initial and replaced hydrates were analyzed via ¹³C NMR spectroscopy and powder X-ray diffraction (PXRD) to examine cage-dependent guest distributions and possible structural transition. To identify heat generation or absorption during the replacement process and to elucidate its influence on the thermal properties of the replaced hydrates, changes in heat flow and dissociation enthalpies (ΔH_d) were measured using a high-pressure micro-differential scanning calorimeter (HP μ-DSC). The replacement behaviors were strongly dependent on the structure of initial gas hydrates. The overall experimental results provide further insights into the cage-specific occupation of external gas molecules and thermodynamic stability for the real replacement occurring in natural gas hydrate reservoirs for CH₄ recovery and CO₂ sequestration.