Abstract: The Shaya Uplift, an important structural belt in the northern Tarim Basin, northwestern China, has been regarded as a thrust belt. However, this recognition is not only incompatible with the flower structures on the seismic profiles, but also contradictory with the fault distribution in a broom or trailer mode in plan view. High-resolution 3D seismic profiles indicate that a two-stage strike-slip structural deformation happened in the Shaya Uplift. The first is from the Late Caledonian to the Indosinian, in which transpressional deformation occurred and a huge positive flower structure was thus formed in the deeper part, and strata were eroded because of the structural uplifting. The second is during the Himalayan, in which a negative inverted/transtensional deformation occurred and a negative flower structure was formed in the shallower part. These results indicate that it is not a uniform tectonic-sedimentary environment in the northern Tarim because of the Shaya Uplift barrier and that the Late Caledonian and the Early Himalayan may be two important structural transformation periods.