We employed a tunneling enabled hopping model to investigate the charge transport properties for four n-type organic semiconductors perylene diimides compounds. The molecular parameters are calculated by density functional theory and the transport is modeled by kinetic Monte Carlo simulation. It is found that the substitutions at the bay positions of the perylene core have large influences on the charge transport properties through modifications in molecular conformation, the charge reorganization energy as well as the stacking networks in the crystals. The temperature dependence of the mobility shows typical “band-like”, in agreement with the recent experiment, but we ascribe it to be the characteristic of nuclear tunneling effect for a localized charge, not by a delocalized band. The largest charge mobility is calculated to be 16.96 cm2/V s for the cyano substitution, in good comparison with the experimental value of 6 cm2/V s.