We present a theoretical study of the stacking properties of poly(3-hexylthiophene) (P3HT) and its effect on the electronic and transport properties. Our study is based on ab initio density functional calculations including van der Waals interactions and molecular dynamics simulations. Our calculations provide detailed information of the atomic structures and the formation mechanisms of the particular stacking structures. We found the most stable stacking structure produces a relatively small hole effective mass in the stacking direction, which allows large interchain mobility.