We investigated annealing and thickness related performance and degradation of bulk heterojunction solar cells based on regioregular poly(3-hexylthiophene) (RR-P3HT):[6,6]-phenyl C61-butyric acid methyl ester (PCBM). The devices were fabricated with slow drying for different active layer thicknesses (100–200nm thick), followed by an identical thermal annealing. Photoinduced charge carrier generation and dissociation as well as series resistance were extracted from the device current–voltage characteristics and correlated to the active layer absorbance and morphology to understand the behavior of the fabricated devices. It was observed that with slow drying method the thickest absorber device had the highest efficiency but upon the followed thermal annealing it degraded while the thinnest one became substantially improved in performance. For the degraded device the charge carrier generation rate was found nearly unreduced, while the dissociation probability at maximum power voltage and series resistance largely deteriorated with thermal annealing. This implies a likely hampered charge transport and increased recombination losses with a discontinuation of the bi-phase networks caused by a further phase separation in the heat treatment. Thus, morphology control for effective charge transport appears crucial to the device performance and stability, and taking into account the active layer thickness effect in annealing is important.