We examined the molecular alignment and nanostructure of 1,4,5,8,9,11-hexaazatriphenylene-hexanitrile (HATCN) thin films grown on organic surfaces using the grazing incidence wide angle X-ray scattering method. HATCN molecules were found to be stacked with a (00l)hex preferred orientation on organic surfaces and the orientation was maintained with increasing thickness, in contrast to growth on metal surfaces. The structural factor from the grazing incidence small-angle X-ray scattering measurement indicated that the HATCN films were formed with regularly distributed nanograins on a hydrophobic organic surface. The nanograins maintained their arrangement, even after forming a transparent electrode on the HATCN film via a sputtering process. The preferential ordering of HATCN on three different electron transporting organic materials was further examined. HATCN displayed the highest crystallinity on the 4,7-diphenyl-1,10-phenanthroline (Bphen) layer.