The thermal evolution of the nano-grain structure and surface of ultra thin copper(II) phthalocyanine (CuPc) films was investigated by real time grazing incidence small angle X-ray scattering (GI-SAXS) and X-ray reflectivity measurements. The evolution was strongly affected by the substrate surface energy. On hydrophilic Si, CuPc film consisted of disk shaped nano-grains of two different sizes. The larger grains showed lateral crystal growth and planarization by thermal annealing, while the smaller grains did not increase in size. The grains formed clusters at high temperature. On hydrophobic Si, CuPc nano-grains are more randomly distributed. The crystal size did not increase in size upon thermal annealing. Thermal annealing induced a more random distribution of nano-grains with an increase in roughness, and large islands formed by the coalescence of small grains. The different thermal evolution models of CuPc films based on GI-SAXS analysis are consistent with the different temperature behavior of the hole mobilities of organic field-effect transistor (OFET) devices fabricated on both surfaces.