As a clean, low-carbon energy source, shale gas presents significant potential with the global population and energy consumption continue to rise. However, the recovery of shale gas depends on the flow characteristics of gas within the organic nanopores of shale. The complex pore structure, particularly the presence of kerogen, causes the gas flow mechanisms to differ from those in conventional reservoirs. This study uses molecular dynamics (MD) simulations to investigate the flow characteristics of methane in rough graphene nanopores and analyzes the effects of pore size and pressure on gas transport behavior. Simulations were performed using LAMMPS software, with conditions including different pore sizes (5–9 nm) and pressures (15–35 MPa). After obtaining equilibrium structures through GCMC simulations, both equilibrium molecular dynamics (EMD) and non-equilibrium molecular dynamics (NEMD) simulations were conducted. The results show that methane flows faster in smooth nanopores, with a significant surface slip effect. However, as roughness increases, the slip effect diminishes, and the flow transitions to viscous behavior. Additionally, pore size has a crucial impact on flow characteristics, with larger pores facilitating faster flow, while increased pressure leads to higher flow rates and longer slip lengths. This study provides essential theoretical insights into the flow of gas in complex nanopores during shale gas recovery, contributing to the optimization of shale gas extraction technologies.