The multiple-scattering cluster (MSC) method is employed to calculate the S 1s near edge x-ray absorption fine structure (NEXAFS) of single dihexyldisulfide molecule and dihexyldisulfide multilayer. The local structure model of the dihexyldisulfide multilayer is proposed. The MSC calculation shows that the neighboring dihexyldisulfide molecules are parallelly arranged in an ordered square cross section with side of 0.47 nm. The discrete variational Xα method is employed to calculate the electronic structure of the single molecule and multilayer, which confirms the MSC results, and reveals the physical origin of all the features in the S 1s NEXAFS spectrum. The analysis of the interaction between the dihexyldisulfide molecules shows that the local structure of the multilayer has the property of self-assemblage.