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The correlations between the chemical structures of the 2,5-diphenyl-1,3,4-oxadiazole compounds and their corresponding vapour deposited film structures on Si/SiO2 were systematically investigated with AFM, XSR and IR for the first time. The result shows that the film structure depends strongly on the substrate temperature (Ts). For the compounds with ether bridge group, the film periodicity depends linearly on the length of the aliphatic chain. The films based on those oxadiazols have ordered structure in the investigated substrate temperature region, while die amide bridged compounds form ordered film only at high Ts due to the formation of intermolecular H-bond. The tilt angle of most molecules is determined by the pi-pi complexes between the molecules. The intermolecular interaction between head groups leads to the structural transformation during the thermal treatment after deposition. All the ether bridged oxadiazoles form films with bilayer structure, while amide bridged oxadiazole form film bilayer structure only when the molecule has a head group.