Understanding and characterizing the transport of shale gas (methane) through the nanopores of kerogens are critical for the accurate prediction of shale gas recovery. However, the key factors that regulate shale gas transport through highly roughened nanopores of shale kerogens are not fully understood. In this work, methane transport in organic nanopores with a high relative roughness is characterized using equilibrium and non-equilibrium molecular dynamics methods. According to our results, the CH4 mass flux has a linear relationship with the pressure gradient, consistent with previous studies, while the calculated slip lengths and gas fluxes varied with different roughness geometries in the order of sigmoidal ≥ triangular > rectangular. Surface slip flow can be a major contributor to the overall gas flux, but surprisingly, the relative contribution of surface slip flow is independent of the pressure gradient. In contrast, the contributions of both slip flow and the average gas fluxes vary strongly with pore diameters. Typical contributions of the adsorbed layer to the overall gas flux are in the range 20–40% but vary from as high as 74% in a 4-nm pore to as low as 6% in a 16-nm pore. Compared to smooth nanopores, we find that, in nanopores with realistically high degrees of relative roughness, methane confinement in cavities decouples slip flow from the flow in the pore interior, significantly reducing the overall flux.