Large amounts of CH4 in the form of solid hydrates are stored on continental margins and in permafrost regions. If these CH4 hydrates could be converted into CO2 hydrates, they would serve double duty as CH4 sources and CO2 storage sites. Herein, we report the swapping phenomena between global warming gas and various structures of natural gas hydrate including sI, sII, and sH through 13C solid-state nuclear magnetic resonance, and FT-Raman spectrometer. The present outcome of 85% CH4 recovery rate in sI CH4 hydrate achieved by the direct use of binary N2 + CO2 guests is quite surprising when compared with the rate of 64 % for a pure CO2 guest attained in the previous approach. The direct use of a mixture of N2 + CO2 eliminates the requirement of a CO2 separation/purification process. In addition, the simultaneously-occurring dual mechanism of CO2 sequestration and CH4 recovery is expected to provide the physicochemical background required for developing a promising large-scale approach with economic feasibility. In the case of sII and sH CH4 hydrates, we observe a spontaneous structure transition to sI during the replacement and a cage-specific distribution of guest molecules. A significant change of the lattice dimension due to structure transformation induces a relative number of small cage sites to reduce, resulting in the considerable increase of CH4 recovery rate. The mutually interactive pattern of targeted guest-cage conjugates possesses important implications on the diverse hydratebased inclusion phenomena as clearly illustrated in the swapping process between CO2 stream and complex CH4 hydrate structure.