Morphological characterization has been used to explain the previously observed strong correlation between charge carrier mobility measured with thin-film transistors and the number-average molecular weight (MW) of the conjugated polymer regioregular poly(3-hexylthiophene). Atomic force microscopy and X-ray diffraction show that the low-mobility, low-MW films have a highly ordered structure composed of nanorods and the high-mobility, high-MW films have a less ordered, isotropic nodule structure. Modifying the morphology for a constant MW by changing the casting conditions or annealing the samples strongly affects the charge transport and morphology in the low-mobility, low-MW films, but has little effect on the high-MW films. In-plane grazing incidence X-ray scattering shows the in-plane pi-stacking peak increases when the mobility increases for a constant MW. When the MW is changed, this correlation breaks down, confirming that in-planet-stacking does not cause the mobility-MW relationship. We believe a combination of disordered domain boundaries and inherent effects of chain length on the electronic structure cause the mobility-MW relationship.