Charge transport in an organic semiconductor is strongly dependent on the molecular packing motif, which could be modified by the molecular substitutions and molecular isomerization. We constructed a series of benzodithiophene-based organic semiconductor molecules with different silyethyne substitutions and isomers. The existence of different conformations of these molecules is supported by a low isomerization energy barrier from density functional theory. By using Marcus semiclassical theory calculation, we make a comprehensive assessment for the effect of molecular substitution and isomerization on charge transport. We found that the hole mobility of cis-isomer molecular packing can be enhanced by increasing the length of silylethyne substitutions. We demonstrated that a favorable charge-transport material would possess an identical direction of induced ring currents, stable induced magnetic fields, and dominant π–π stacking interaction in their molecular packing motif to ensure good π-overlap area. Our findings will provide direct guidance for developing organic semiconductor materials.