Real time variation of the interfacial structure between an Al electrode and a poly(3-hexylthiophene) (P3HT):fullerene (PCBM) thin film during thermal annealing has been investigated using synchrotron X-rays. It is found that Al atoms diffuse into the organic layer to form a thin interlayer between the Al electrode and the organic layer even during the deposition of an Al layer. The interlayer thickness and the mass density of the interlayer increases if annealed above 120 degrees C. The interlayer thickness depends on the annealing processes and the inter-diffusion is accelerated by a fast annealing process. The Al diffusion reduces the preferred alignment of the (100) direction of the P3HT crystals from the surface normal direction and randomizes their orientation. The Al diffusion also helps to reduce the contact resistance in the P3HT:PCBM-based solar cells.