Abstract: To study the adsorption and diffusion behaviors of CO₂ on the rough coal matrix surface during CO₂ geological sequestration in deep coal seams from a microscopic perspective, and to reveal the mechanism of the effect of three-dimensional surface roughness on CO₂ storage and transport in coal, this study first obtained roughness data of nanopore surface of coal based on atomic force microscopy (AFM) testing, and proposed a new method for constructing three-dimensional rough surface by combining molecular simulation technology. Then, a more realistic three-dimensional surface rough anthracite model was constructed to explore the differences and underlying mechanisms of adsorption and diffusion behaviors of CO₂ on different rough surfaces at temperature of 318 K and pressure of 0−20 MPa. The results show that: ① The surface roughness has a more significant effect on CO₂ adsorption in micropores. Compared with the smooth surface, the rough surface can enlarge the CO₂ adsorption area (3.08 times for 1 nm slit pore, 1.30 times for 3 nm slit pore, and 0.73 times for 6 nm slit pore), increase the average density of CO₂, accelerate the adsorption rate of CO₂, and facilitate the adsorption saturation of CO₂ at low pressure. Meanwhile, the surface roughness can also promote the transformation of CO₂ adsorption configuration from smooth rectangle to concave convex shape, which has a significant impact on the distribution pattern of CO₂ occurrence. ② In the rough-surfaced coal matrix slit nanopore system, due to the superposition effect of the adsorption force field, groove space can form lower-energy adsorption sites, thereby enhancing gas-solid and gas-gas interactions and increasing the adsorption capacity in this area. ③ The surface roughness is negatively correlated with the horizontal diffusion coefficient of CO₂, while the pore size is positively correlated with the horizontal diffusion coefficient of CO₂. ④ The adsorption potential of CO₂ in the rough coal matrix shows a multi-peak distribution, and rough coal matrix is more conducive to the stable adsorption and storage of CO₂. ⑤ This study can provide theoretical guidance and scientific basis for the more accurate assessment of CO₂ storage potential in deep coal seams, in order to optimize CO₂ storage strategies.