The evolution of nanomorphology within thin solid-state films of poly(3-alkylthiophene):[6,6]-phenyl-C61 butyric acid methyl ester (P3AT:PCBM) blends during the film formation and subsequent thermal annealing is reported. In detail, the influence of the P3AT's alkyl side chain length on the polymer/fullerene phase separation is discussed. Butyl, hexyl, octyl, decyl, and dodecyl side groups are investigated. All of the P3ATs used were regioregular. To elucidate the nanomorphology, atomic force microscopy (AFM), X-ray diffraction, and optical spectroscopy are applied. Furthermore, photovoltaic devices of each of the different P3ATs have been constructed, characterized, and correlated with the nanostructure of the blends. It is proposed that the thermal-annealing step, commonly applied to these P3AT:PCBM blend films, controls two main issues at the same time: a) the crystallization of P3AT and b) the phase separation and diffusion of PCBM. The results show that PCBM diffusion is the main limiting process for reaching high device performances.