CH₄–CO₂ replacement technology has broad application prospects in reducing CO₂ emission and developing natural gas hydrate (NGH) resources. It is of great significance to study the mechanism of CH₄–CO₂ replacement. In this paper, the effect of H₂O on CH₄–CO₂ displacement behavior is studied by molecular dynamics (MD) simulation and quantum mechanics calculation. The interactions between the host and guest in cages of CH₄ hydrate are calculated using the symmetry-adapted perturbation theory method. The contribution of physical components of binding energy can be determined. The result indicates that the electrostatic interaction of H₂O–H₂O and H₂O–gas is a key factor of the CH₄–CO₂ replacement mechanism. Additionally, the microconfigurations and microstructure properties are analyzed by MD simulation in the systems containing a gas layer (CO₂ or CH₄) and a CH₄ hydrate layer. The results showed that the movement and the arrangement of H₂O molecules influence the hydrate structure due to the interaction of H₂O–gas during the replacement process. The molecular simulation suggests that the change of electrostatic interaction with H₂O molecules could improve the CH₄–CO₂ replacement efficiency, which can be favorable for the investigation of CH₄ replacement technology in NGH with CO₂ injection.