The complex deformation styles of large intraplate strike-slip fault systems in the multi-stage superimposed basin are hot topics worldwide. This article proposes structural models and evolution processes for such strike-slip fault systems in the Tarim Basin based on high-resolution 3D seismic data and deep wells. Our analyses reveal that strike-slip fault in the Tarim Basin formed with different structural styles in five tectonic layers from the Sinian to the Permian that accompanies the Sinian rift systems and uplift, the Lower–Middle Cambrian reversed faults and salt tectonics, the Ordovician fault-karst systems, the Silurian to the Carboniferous en-echelon transtensional faults, and the Permian volcanic structures. Influenced by the multi-tectonic layers and complex evolution history, the strike-slip faults performed as multi-layer flower structures and various fault types. The evolution history of paleo-uplifts also influenced the distribution characteristics of strike-slip faults, such as X, diamond, and V shapes in the Tabei uplift and T shapes in the Tazhong uplift. The strike-slip faults formed in late Cambrian stage were associated with unconformities, inverted structures, and growth strata in deep layers. The different tectonic evolution models of the Tabei and the Tazhong uplift were built, which shows pre-existing structures, the lithological combinations from the rift basin to the marine basin, and the change of regional tectonic stress from the Cambrian to Permian are controlling factors of the strike-slip fault systems. These models provide a new interpretation method for intraplate strike-slip fault systems worldwide.