The charge transport properties of a series of rubrene derivatives were systematically investigated by density functional theory and molecular dynamics (MD) simulations. It was found that functionalizing electron-withdrawing groups (-CN, -CF3, or fluorination) on the peripheral phenyls not only enhance the chemical stability of materials but also favor electron injection by lowering the energy levels of frontier molecular orbitals and increasing the electron affinities. Derivatives 2-5 and 9, exhibiting packing motifs similar to rubrene but closer pi-stacking distances, possess large hole and electron-transfer integrals, significant bandwidths, and small effective masses, suggesting excellent ambipolar semiconductor behavior. The maximum hole(electron) mobilities in the Marcus hopping mechanism based on kinetic Monte Carlo simulation can reach 14.0-16.5(1.6-3.5) cm(2) V-1 s(-1). Interestingly, the antiparallel 2-D brick stacking and twisted backbones of fluorinated derivatives 11 and 12 result in nearly 1-D percolation network but balanced hole and electron transport property. In contrast, the parallel 2-D brick stacking of 14 leads to 2-D percolation network. Their maximum hole and electron mobilities fall in the range of 0.5-3.6 and 2.0-4.8 cm(2) V-1 s(-1). Furthermore, MD simulations show that dynamic disorder is strongly detrimental to the hole transfer but has a little influence on the electron transfer for 1-5. Moreover, severe twist of backbones of 9 leads to almost 1 order of magnitude lowered mobility. In addition, the influences of different substituents on the molecular structure, packing motif, and intermolecular reorganization energy are discussed.