Diffraction contrast tomography using ultrabright synchrotron radiation X-rays was performed on an austenitic stainless steel with a bimodal harmonic structure in which a network structure of fine grains (Shell) surrounds a coarse grain structure (Core). Then, not only were the shape and position of each grain reconstructed, but the change in excess dislocation density during the fatigue process, Δρ, was also measured. The results show that Δρ depends on the diffraction plane, Schmidt factor, and grain size, and that the change in Δρ during the fatigue process of a harmonic structured material is less than that of a conventional material. This result indicates that the network of fine grains in the harmonic structure supports microdeformation and suppresses the deformation of coarse grains. Furthermore, it was found that Δρ of grains unrelated to crack initiation increased continuously with the number of cycles, whereas that around the crack initiation site decreased with crack initiation.