Up to date, for the purpose of simplicity, graphene-based structures, like nano-porous carbons or carbon nanotubes, have been widely utilized to investigate methane flow behavior inside shale organic nanopores. However, realistic shale organic matrix is composed of kerogen molecules, possessing complex amorphous structures and apparently different surface attributes compared with graphene-based nanopore surface, which will inevitably have a great impact on surface-methane interactions and methane flow behavior. Current research works in terms of the graphene-based material fails to capture the influence of kerogen surface, and therefore cannot accurately characterize nano-confined methane flow behavior through realistic shale organic matter. Also, shale organic nanopores with different kerogen types contain different surface compositions, while its impact on methane flow capacity has not been reported yet. To bridge this knowledge gap, this paper simulates the methane flow behavior through authentic kerogen-based circular nanopores with the use of molecular dynamics (MD) for the first time. And a novel construction method was developed to generate kerogen-based organic nanopores with desirable pore size and different kerogen types for MD simulation. Main results show that a) decrease in pore size will contribute to the enhancement of adsorption capacity for nanopores and type-III kerogen > type-II kerogen > type-I kerogen in terms of methane adsorption capacity; b) ratio of average methane density confined in nanopores to bulk-gas density ranges from 1.2 to 2.6, which will decrease with the increase of the pressure and increase with decreasing pore size; c) Under shale geological condition, the conventional theoretical model for nanoconfined gas flow will underestimate that of 0.41 time for type-I kerogen-based nanopores, 0.59 time for type-II kerogen-based nanopores, and 0.88 time for type-III kerogen-based nanopores.