Coalbed methane has garnered increased attention from researchers due to its potential for efficient development and utilization. In this study, the roughness data of coalbed pore surfaces were first obtained using atomic force microscopy tests. A novel method for constructing three-dimensional rough surfaces was proposed by combining these data with molecular simulation technology. Consequently, a more realistic three-dimensional coalbed surface roughness model was built, and the influence of surface roughness on CH4 adsorption and diffusion was explored. The results show that the CH4 adsorption configuration on coalbed nanopore surfaces is closely related to surface roughness. The grooves formed by the rough surface provide more adsorption space for CH4 storage. CH4 preferentially adsorbs in these grooves, forming intermittent adsorption layers. The adsorption capacity of the coal matrix slit nanopore system with rough surface is as follows: the groove part of the groove space > the surface part of the groove space > the convex surface part of the coal matrix > the convex part of the groove space > the middle part of the slit nanopore. CH4 average adsorption density increases with greater surface roughness and smaller pore size. Pore size is the main factor controlling CH4 diffusion; larger pores promote diffusion, while increased surface roughness hinders diffusion. Differences in CH4 diffusion coefficients due to surface roughness tend to equalize under high pressure. The analysis of the potential energy and average heat of adsorption indicates that CH4 adsorption is more stable under conditions of rough surfaces, small pore sizes, and high pressure.