We investigated the evolution of quaterrylene thin films on SiO2 and on an octadecyltrichlorosilane self-assembled monolayer (OTS-SAM) to examine the impact of film strains on the growth processes and evolving structure. Surface modification by SAMs allowed tailoring of the growth process from a Stranski–Krastanov (SK) mode (layer-plus-island) on the SiO2 surface to a Frank–van der Merwe mode (layer-by-layer) on the OTS surface. Detailed structural analysis by x-ray diffraction techniques confirmed that the SK mode was driven by lattice strain in the initial wetting layers on the SiO2 surface. On the other hand, strain-free wetting layers were already formed at the beginning of growth on the OTS surface, thereby suppressing three-dimensional island formation. Moreover, the films on the SiO2 surface were found to incorporate high microstrain induced by crystal defects such as dislocations and a mosaic structure. In contrast, few crystal defects were present in the films on OTS surface, demonstrating that OTS treatment enables marked improvement of the molecular alignment. These results clearly indicate that the lattice strain induced by the molecular-substrate interaction is essential for controlling the overall growth process.