Highly metamorphic coal plays a significant role in China's energy development plan owing to its high calorific value. Its complex organic composition provides outstanding storage capabilities for methane (clean and efficient unconventional natural gas), which leads to terrible gas outburst hazards. Minimizing the main storage sites of CH4 (micropores) through organic solvent extraction provides an efficient and safe route for exploiting coal and natural gas energy sources. This phenomenon can be elucidated by the removal of the chemical components that have an adverse impact on the micropore filling theory. In this study, we constructed macromolecular models of highly metamorphic coal, and relative dynamic simulations under experiment and field conditions are performed. The corresponding CH4 storage capacity and spatial coordination distribution of the coal after five treatments were derived. Combined with the results of the micropore filling theory, it was shown that the equilibrium distance of CH4 filling in the micropore increased with the degree of extraction (from 0.351 nm for XT to 0.572 nm for XT-DMF). Also, the trend of CH4 adsorption position in the representative samples (the number of monolayer affixations decreased from 10 to 9) provides crucial support for the conclusions, and the low-potential region with a high potential difference contributes to CH4 stability. The breakthrough of this study will provide strong support and a solid theoretical basis for the efficient and safe exploitation of CBM (Coalbed methane) energy resources.