Based on 3D seismic and drilling data, the timing, evolution and genetic mechanism of deep strike-slip faults in the central Sichuan Basin are thoroughly examined by using the U-Pb dating of fault-filled carbonate cement and seismic-geological analysis. The strike-slip fault system was initially formed in the Late Sinian, basically finalized in the Early Cambrian with dextral transtensional structure, was overlaid with at least one stage of transpressional deformation before the Permian, then was reversed into a sinistral weak transtensional structure in the Late Permian. Only a few of these faults were selectively activated in the Indosinian and later periods. The strike-slip fault system was affected by the preexisting structures such as Nanhuanian rifting normal faults and NW-striking deep basement faults. It is an oblique accommodated intracratonic transfer fault system developed from the Late Sinian to Early Cambrian to adjust the uneven extension of the Anyue trough from north to south and matches the Anyue trough in evolution time and intensity. In the later stage, multiple inversion tectonics and selective activation occurred under different tectonic backgrounds.