Adsorbed methane in shale organic nanopores is an important factor of the shale gas resource. The major component of shale organic matter, kerogen solids, consists of macro organic molecules and functions as the most important adsorbent. In this work, a novel molecular simulation workflow is proposed to generate organic pores on residue-type kerogen molecules and to simulate the gas adsorption in the pores. The molecular dynamics-based cutter atom pore generation method can construct pores with arbitrary shapes and sizes-approaching microscopy observations-2-50 nm shale matrix pores with reasonable physical significance. Grand canonical Monte Carlo simulations for CH4 and CO2 are performed on kerogen pores with various pore radii using two categories of molecular potentials. The ensemble averaging density distributions in the pores are calculated and analyzed, which concludes that the free gas state becomes distinguishable from the adsorbed state unless the pore radius exceeds 1 nm. Adsorbed layers at the kerogen pore surfaces are heterogeneous because of non-uniformly distributed adsorptive sites on the surfaces. Adsorption isotherms are simulated and thereafter fitted with the Langmuir equation comparing various molecular models and fluid types. The adsorption affinity indicated by the Langmuir pressure for the total adsorbed molecule number in all cases decreases as a function of increasing pore size. (C) 2016 Elsevier Ltd. All rights reserved.