The diffusion characteristics of CH4, CO2, and N2 in coal are important for the study of CO2-enhanced coalbed methane (CO2-ECBM) recovery, which has become the most potential method for carbon sequestration and natural gas recovery. However, quantitative research on the diffusion characteristics of CH4 and the invasive gases (CO2 and N2) in coal, especially those in micropores, still faces enormous challenges. In this paper, the self-, Maxwell’s, and transport diffusions of CO2, CH4, and N2 in mid-rank coal vitrinite (MRCV) macromolecules were simulated based on the molecular dynamics method. The effects of the gas concentration, temperature, and pressure on the diffusion coefficients were examined via the comparison of various ranks. The results indicated that the diffusion coefficients have the order of D(N2) > D(CO2) > D(CH4) in their saturated adsorption states. However, when MRCV adsorbed the same amounts of CH4, CO2, and N2, the self- and transport diffusion coefficients followed the order of DS(N2) > DS(CO2) > DS(CH4) and Dt(CO2) > Dt(N2) > Dt(CH4), respectively. Independent of the gas species, all these diffusion coefficients decreased with increasing gas concentration and increased with increasing temperature. In the saturated adsorption state, the diffusion activation energies of CH4, CO2, and N2 were ordered as CH4 (27.388 kJ/mol) > CO2 (11.832 kJ/mol) > N2 (10.396 kJ/mol), indicating that the diffusion processes of CO2 and N2 occur more easily than CH4. The increase of temperature was more conducive to the swelling equilibrium of coal. For the pressure dependence, the diffusion coefficients first increased until the peak pressure (3 MPa) and then decreased with increasing pressure. In contrast, the diffusion activation energy first decreased and then increased with increasing pressure, in which the peak pressure was also 3 MPa. The swelling rate changed more obviously in high-pressure conditions.