Perylene diimides (PDIs) and their derivatives are active n-type semiconducting materials widely used in organic electronic devices. A series of PDI derivatives have been investigated by quantum chemistry calculations combined with Marcus–Hush electron-transfer theory. The substitution of three different sites of a PDI induces large changes in its electron-transfer mobility. 2,5,8,11-Tetrachloro-PDI with four chlorine atoms in ortho positions shows both large electron- and hole-transfer mobilities of 0.116 and 0.650 cm2 V−1 s−1, respectively, indicative of a potentially highly efficient ambipolar organic semiconducting material. The calculated electron-transfer mobility of 1,6,7,12-tetrachloro-PDI is 0.081 cm2 V−1 s−1, which is in good agreement with the experimental result. Octachloro-PDIs have the largest electron mobility among these derivatives, although the π system of the central core is twisted. 2D π-stacking and hydrogen bonds formed at the imide positions are responsible for the large mobility. Simulated anisotropic transport mobility curves of these materials prove the magnitude of the mobility that appears when the measuring transistor channel is along the a-axis of the crystal, which is the direction of hydrogen bond formation.