The influence of various thermal treatment steps on the morphology and the photoconductive properties of a non-contacted, 50 nm thick blend (50:50 wt.-%) of [6,6]-phenyl C61-butyric acid methyl ester (PCBM) and poly(3-hexyl thiophene) (P3HT) spin-coated from chloroform has been studied using transmission electron microscopy (TEM) and the electrodeless time-resolved microwave conductivity technique. After annealing the film for 5 min at 80 °C, TEM images show the formation of crystalline fibrils of P3HT due to a more ordered packing of the polymer chains. The thermal treatment results in a large increase of the photoconductivity, due to an enhancement of the hole mobility in these crystalline P3HT domains from 0.0056 cm2 V–1 s –1 for the non-annealed sample to 0.044 cm2 V–1 s –1 for the sample annealed at 80 °C. In contrast, the temporal shape of the photoconductivity, with typical decay half-times, τ1/2, of 1 μs for the lowest excitation intensities, is unaffected by the temperature treatment. Further annealing of the sample at 130 °C results in the formation of three different substructures within the heterojunction: a PCBM:P3HT blend with PCBM-rich clusters, a region depleted of PCBM, and large PCBM single crystals. Only a minor increase in the amplitude, but a tenfold rise of the decay time of the photoconductivity, is observed. This is explained by the formation of PCBM-rich clusters and large PCBM single crystals, resulting in an increased diffusional escape probability for mobile charge carriers and hence reduced recombination.