Nowaday nanocrystalline materials due to their unique mechanical and physical properties, have been considered by many researchers. These different properties are result of very low grain size of these materials ( 100 nm) which creates high fraction of grain boundary regions. Preservation of such characteristics depends on the grain size stability (at nanoscale) of this materials that is affected by processes such as relaxation, grain boundary migration and grain growth. However, the self diffusion is known as a affective factor that affecting the structural changes. Hence, understanding of self diffusion can be useful in stability materials. Due to many difficulties of experimental evaluation of this process, it is felt necessary, using simulation techniques. Therefore, in this study, molecular dynamics simulation was used to study of self diffusion in the nanocrystalline iron. Because of the difficulties of separating the different parts of nanocrystalline and structural changes during diffusion process, limited simulation efforts have been made by nanocrystalline that contai grains with actual size. Also, with regard to the different nature of diffusion process in different parts of grain boundary, such as triple junction lines and quad node points, Accurate consideration of this parts must be take into account. In this research, by presenting a method for separating different parts of nanocrystalline and considering influence of structural changes, diffusion coefficients of all parts of nanocrystalline for different grain size and different temperature were calculated. Additionally, by using diffusion coefficients at different temperatures, the activation energy and diffusion prefactor of different parts of nanocrystalline Fe ware calculated. It was observed that the diffusion coefficient in nanocrystalline grains was less than grain boundaries and whole of nanocrystalline. On the other hand, diffusion coefficients in grain boundary is less than triple junction lines at all temperatures and all grain sizes. By changing in grain size, diffusion coefficients in grain boundary parts, has no significant change but with increasing nanocrystalline grain size, diffusion coefficients decrease in grain and total nanocrystalline. The activation energy and diffusion prefactor depends on the parts, has different behavior. so that the activation energy of grain boundary part was approximately equal but diffusion prefactor in the triple junction lines has higher values. In the various parts of the nanocrystalline, activation energy and diffusion prefactor increase with increasing in grain size. It was observed that there is a direct relation between excess volume and activation energy. Due to high fraction of grain boundary regions in nanocrystalline Fe, activation energy of diffusion is lower than coarse grain Fe and diffusion in nanocrystalline is much faster than coarse grain. Keywords: Nanocrystalline Fe, grain boundary, triple junction regions, grain boundary regions, self diffusion, diffusion coefficient, activation energy, diffusion prefactor.