The elusive and difficult to measure phase separation length scale in poly(3-hexylthiophene):C61-butyric acid methyl ester (P3HT: PCBM) bulk heterojunction layers was measured using small-angle X-ray scattering (SAXS) from thick films of the blend. After drop-casting and allowing the material to dry, there was a distinct nanoscale phase separation of the two blend components as measured by SAXS. Thermal annealing reduced the degree of phase separation as qualitatively measured by the decrease in the SAXS invariant, and the phase separation length scale was virtually unchanged at 25 nm. We attribute this reduction in the SAXS invariant to diffusion of PCBM into the amorphous P3HT; this was also confirmed by a reduction in the photoluminescence (PL) and a small reduction in the PL lifetime. We show that a bulk heterojunction system blend of 1:0.7 P3HT:PCBM is not just a simple two-phase system with well-defined interfaces, but instead it is a much more complicated system incorporating regions of crystalline P3HT, PCBM, and a mixed phase of amorphous P3HT and PCBM. Our work confirms that PCBM penetrates into P3HT upon thermal annealing and so reinforces the view proposed by Kiel et al. [Phys. Rev. Lett. 2010, 105, 168701]. We suggest that, alongside device testing this type of thick film, SAXS experiments would aid efficiency improvements by permitting measurement of the phase separation length scale in bulk heterojunction organic photovoltaic materials. This is a key parameter for understanding and designing improved polymer solar cells.