All conjugated polymers examined to date exhibit significant cumulative lattice disorder, although the origin of this disorder remains unclear. Using atomistic molecular dynamics (MD) simulations, the detailed structures for single crystals of a commonly studied conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT) are obtained. It is shown that thermal fluctuations of thiophene rings lead to cumulative disorder of the lattice with an effective paracrystallinity of about 0.05 in the π–π stacking direction. The thermal-fluctuation-induced lattice disorder can in turn limit the apparent coherence length that can be observed in diffraction experiments. Calculating mobilities from simulated crystal structures demonstrates that thermal-fluctuation-induced lattice disorder even enhances charge transport in P3HT. The mean inter-chain charge transfer integral is enhanced with increasing cumulative lattice disorder, which in turn leads to pathways for fast charge transport through crystals.