Decoupling the molecular structure from the pore structure is challenging under experimental conditions; this hinders the independent investigation of the effect of the changes in molecular structure on methane (CH4) transport. In this study, the molecular model of coal was reconstructed based on the test results of X-ray photoelectron spectroscopy (XPS) and 13C nuclear magnetic resonance (13C NMR). A grand canonical Monte Carlo (GCMC) based molecular dynamics (MD) simulation method was used to independently investigate the effect of CO2 on CH4 adsorption and diffusion behaviour in coal under changes in the molecular structure of coal after ultrasonic excitation. The experimental results show that, under ultrasonic excitation, the proportion of oxygen content in the coal increases and the oxygen-containing functional groups (carboxyl groups, ether bonds/hydroxyl groups) increase compared to the original coal. The simulation results show that the amount of CH4 adsorbed, the isosteric heat and the proportion of low-energy CH4 in the coal sample decrease after ultrasonic excitation for the same pore size. Furthermore, for the same pore size and CO2 partial pressure ratio, adsorption selectivity factor increases after ultrasonic treatment. Additionally, for the same pore size and the same CO2 partial pressure ratio, the interaction energy between CH4 and coal in the CH4–CO2–coal mixed system decreases and the density of high-energy CH4 increases after ultrasonic excitation; this leads to an increase in CH4 self-diffusion and transport diffusion coefficient. The presence of oxygen-containing functional groups causes a significant increase in the electrostatic potential difference between CO2 and coal as compared to that between CH4 and coal, which is the fundamental reason for the change in the effect of CO2 on the adsorption-diffusion behaviours of CH4. Our findings revealed the micro-mechanism of ultrasonic-assisted coalbed methane extraction and demonstrated the effectiveness of ultrasonic-CO2 collaborative technology.