The initial growth modes of ZnPc films is examined, revealing the previously undescribed nanoscale crystal structure evolution and the nanograins of the ZnPc:C60 mixed layers in the thin films. Initially, the ZnPc molecules are stacked in the preferred γ(200) configuration, similar to the structures of CuPc. The ZnPc thin film growth display 2D planar to 3D island growth after the initial compressive strain had relaxed in films 7–8 MLs thick. 3D island formation decreases the prevalence of the preferred ordering in the γ(200) crystals. The ZnPc films consist of randomly distributed ellipsoid nanograins during the initial growth stages. The ellipsoid nanograins transition to an ordered state later in the growth process. Insertion of C60 changes the preferred molecular stacking of ZnPc, and β(100) forms in the ZnPc:C60 layers fabricated at room temperature, which is usually observed at high annealing temperatures (200 °C) in a single ZnPc film. The ellipsoid ZnPc nanograins also retain their shapes in the ZnPc:C60 mixed layers. The formation of β(100) and the presence of ellipsoid nanograins in the mixed layer are related to improvements relative to planar devices in the organic photovoltaic device performance.