Evolution of BP2T films grown at the early stage was investigated using atomic force microscopy (AFM) and X-ray diffraction (XRD). The AFM results demonstrate that the BP2T grown on the SiO2 substrate transformed from a layer by layer growth to island growth when the coverage is higher than 3 ML. The out-of-plane and in-plane X-ray diffraction measurements reveal a phase transition from the thin film phase to the bulk phase suddenly occurs as the growth mode changes. A careful analysis of the structure evolution implies that not only the strain but also the soft matter property of the organic thin films are responsible for the thickness dependent evolution. Moreover, the thickness dependent structure and phase of BP2T films result in different morphologies of ZnPc grown on different layers of BP2T. The ZnPc crystals gradually changed from stripe-like to nanofiber-like, concomitantly with the epitaxy relationships from incommensurate epitaxy to commensurate epitaxy. Conversely, the diversity of ZnPc films also reflects different properties of the BP2T films with different numbers of layer, which cannot be obtained from the AFM or XRD. This study supplies a deeper insight into the thickness evolution of organic thin films and to the weak epitaxy growth.