Using classical molecular dynamics simulations and quantum chemical calculations, the structure and charge-transfer parameters in crystalline poly(3-hexylthiophene) (P3HT) are investigated. The changes in polymer structure with temperature are studied and, by performing DFT calculations on configurations found from MD, the changes in the charge-transfer characteristics are investigated. The system is found to adopt a structure consistent with X-ray diffraction experiments on the so-called type-II polymorph of the poly(3-alkylthiophenes). Upon increasing temperature, a conformational change in the polymer side chains occurs, which is found to lead to increased disorder in the interring torsions, which modulates the charge transfer along the polymer backbone. The intrachain transfer integrals are found to decrease slightly with temperature, while their distribution broadens considerably due to increased thermal motion of the rings. The interchain transfer integrals are found to be appreciable for both nearest and next-nearest neighbor rings. This, taken with the fact that the positions of rings on neighboring chains are strongly correlated, has consequences for the development of more accurate phenomenological charge-transport models, such as variable range hopping models.