Previous investigations of the field-effect mobility in poly(3-hexylthiophene) (P3HT) layers revealed a strong dependence on molecular weight (MW), which was shown to be closely related to layer morphology. Here, charge carrier mobilities of two P3HT MW fractions (medium-MW: Mn = 7 200 g mol−1; high-MW: Mn = 27 000 g mol−1) are probed as a function of temperature at a local and a macroscopic length scale, using pulse-radiolysis time-resolved microwave conductivity (PR-TRMC) and organic field-effect transistor measurements, respectively. In contrast to the macroscopic transport properties, the local intra-grain mobility depends only weakly on MW (being in the order of 10−2 cm2 V−1 s−1) and being thermally activated below the melting temperature for both fractions. The striking differences of charge transport at both length scales are related to the heterogeneity of the layer morphology. The quantitative analysis of temperature-dependent UV/Vis absorption spectra according to a model of F. C. Spano reveals that a substantial amount of disordered material is present in these P3HT layers. Moreover, the analysis predicts that aggregates in medium-MW P3HT undergo a “pre-melting” significantly below the actual melting temperature. The results suggest that macroscopic charge transport in samples of short-chain P3HT is strongly inhibited by the presence of disordered domains, while in high-MW P3HT the low-mobility disordered zones are bridged via inter-crystalline molecular connections.