The molecular orientation of dinaphtho[2,3-b:2′,3′-f]thieno[3,2-b]thiophene (DNTT) thin films on modified silicon dioxide (SiO2) and copper oxide (CuOx) substrates whose surfaces were treated by 6-[(3-trisilanol)propylamino]-1,3,5-triazine-2,4-bis(2-aminoethylamine) (TAS) was investigated using near-edge X-ray absorption fine structure and ultraviolet/X-ray photoelectron spectroscopy. The standing orientation of DNTT was obtained in DNTT/TAS/SiO2 and DNTT/TAS/CuOx. The amount of amorphous region in DNTT/TAS/SiO2 was larger than that in DNTT/TAS/CuOx. The TAS treatment on the substrates formed interfacial dipoles at TAS/SiO2 and TAS/CuOx interfaces by chemical interaction, resulting in the vacuum level shift by −0.9 and −1.2 eV, respectively. Functional groups at the outermost TAS surface were amino groups in TAS/SiO2 and silanol groups in TAS/CuOx. The intermolecular distance of DNTT was widened in DNTT/TAS/SiO2 because of an electrostatic repulsion with nitrogen. The interfacial dipole at the modification layer/substrate interface and functional groups at the modified surface affect the molecular orientation of DNTT thin films on the modification layer.