A unique deformation microstructure introduced by 20% cold rolling in a Ti-25mass%Nb-25mass%Zr (TNZ) Harmonic Structure (HS) alloy has been studied in detail by crystallographic analysis. The HS consists of soft, coarse-grained regions (Core) that are three-dimensionally surrounded by an interconnected network of hard, ultrafine-grained regions (Shell). The {332}<113> deformation twins are observed in the deformation microstructure of the homogeneous grained TNZ alloy compacts with a sinter holding time of 1.8 ks. In contrast, in the deformation microstructure of the TNZ alloy HS compacts with a sintering holding time of 1.8 ks, deformation bands by slip deformation are observed in Core region. In the deformation microstructure of the TNZ alloy HS compact with a sintering holding time of 0 s, a composite deformation microstructure consisting of two types of deformation bands, {332}<113> deformation twins and <110> axial rotation slip bands, is observed in Core region. It is noteworthy that the same HS material has different deformation structures depending on the sintering time. The reason for the formation of different deformation structures is the effect of the diffusion of Fe elements doped by mechanical milling.