This study investigated the structural transformation, guest distributions, and the extent of replacement in CH4 + C3H8-flue gas replacement occurring in sII hydrates via gas chromatography, NMR spectroscopy, and powder X-ray diffraction (PXRD). Simulated flue gas (CO2 (20%) + N2 (80%)) was injected into an sII CH4 (90%) + C3H8 (10%) hydrate for guest exchange. The extent of replacement occurring in CH4 + C3H8-flue gas replacement was much lower than that of CH4 + C3H8-CO2 replacement. Furthermore, 13C NMR spectra and PXRD patterns revealed that unlike CH4 + C3H8-CO2 replacement, CH4 + C3H8-flue gas replacement did not undergo any structural transformation during the replacement (i.e., iso-structural replacement in the sII hydrate). Rietveld refinement of PXRD patterns of gas hydrates after replacement using flue gas injection demonstrated that CO2 molecules occupied both the small (512) and large (51264) cages, whereas N2 molecules occupied only the small (512) cages. CO2 and N2 were not complementary but competitive in replacing CH4 in the small (512) cages, which contributed to the maintenance of the cage stability of the initial sII hydrate and thus, resulted in a lower extent of replacement. The experimental results obtained in this study provide valuable insights on the accurate replacement mechanism and cage-specific guest exchange behavior of sII hydrates using flue gas injection for energy recovery and CO2 sequestration.