A comprehensive quantitative grasp of methane (CH 4 ), nitrogen (N 2 ), and their mixture's adsorption and diffusion in MIL-101(Cr) is crucial for wide and important applications, e.g., natural gas upgrading and coal-mine methane capturing. Previous studies often overlook the impact of gas molecular configuration and MIL-101 topology structure on adsorption, lacking quantitative assessment of primary and secondary adsorption sites. Additionally, understanding gas mixture adsorption mechanisms remains a research gap. To bridge this gap and to provide new knowledge, we utilized Monte Carlo and molecular dynamics simulations for computing essential MIL-101 properties, encompassing adsorption isotherms, density profiles, self-diffusion coefficients, radial distribution function (RDF), and CH 4 /N 2 selectivity. Several novel and distinctive findings are revealed by the atomiclevel analysis, including (1) the significance of C�C double bond of the benzene ring within MIL-101 for CH 4 and N 2 adsorption, with Cr and O atoms also exerting notable effects. ( 2) Density distribution analysis reveals CH 4 's preference for large and medium cages, while N 2 is evenly distributed along pentagonal and triangular window edges and small tetrahedral cages. (3) Calculations of self-diffusion and diffusion activation energies suggest N 2 's higher mobility within MIL-101 compared to CH 4 . (4) In the binary mixture, the existence of CH 4 can decrease the diffusion coefficient of N 2 . In summary, this investigation provides valuable microscopic insights into the adsorption and diffusion phenomena occurring in MIL-101, thereby contributing to a comprehensive understanding of its potential for applications, e.g., natural gas upgrading and selective capture of coal-mine methane.