Two stages of structural evolution were recognized in the Altun fault zone, which created flower structures in varied crustal levels with different features. The existence of fault breccias, fault zones and fault groups suggested a faulting in the upper crustal level. Meanwhile, it was indicated, by occurrence of the mylonites, related structures and metamorphic rock associations in the fault zone, that the faulting experienced a stage of evolution in the middle crustal level. A later stage flower structure was evidenced by fault groups, striae on fault planes and related joints, while the earlier stage flower structure was characterized by strain indicators in the mylonites, such as occurrence variation of the mylonitic foliations, types, fabric patterns and strain patterns of tectonites. The 40Ar-39Ar dating and geothermometer-geobarometer estimation revealed that the former was a superimposition event about 46 Ma ago, and the latter a ductile faulting about 91～89 Ma ago, accompanied with low-grade metamorphism (temperature 270～500 ℃ and pressure 0.05～0.45 GPa). The co-occurrence of two stages of flower structures might suggest the multistage development and inheritance of development of regional strike-slip faulting due to the continent-continent collision between the Eurasia and Indian plates. The strike-slip faulting along the main fault recorded the eastward regional creeping, and the development of two stages of flower structures and related thrusting on both sides provided chances for regional uplifting and for upwelling of deep crustal materials.