The Neoproterozoic supercontinent breakup is of significant role in the origin of the rift basin and its hydrocarbon on Earth. However, there is still debate on whether the superplume or subduction process has triggered the rift basin. The largest Sinian gasfiled in China has been found along the Deyang-Anyue rift in the Sichuan Basin. Owing to absence of geological data and low-resolution seismic data, it is an enigma on the origin and distribution of the pre-Sinian rifts in the ultra-deep subsurface. Together with seismic interpretation and compiled geochemical data, we discuss the characteristics and mechanism of the pre-Sinian rift in the Sichuan Basin. The results show that: (1) NE-trending Pre-Sinian rifts developed well with more than 5000 m thick deposits in the Sichuan Basin, which are different in rift architecture and distribution from the Sinian depression to show a Pre-Sinian tectonic discontinuity; (2) the ?Hf isotope values of the Neoproterozoic zircons show a distinct pattern from a decreased trend to an increased trend, and present a tectonic transition period at ca. 830~780 Ma; (3) the Pre-Sinian rifting initiated during the transition period was consistent subduction process rather than mantle plume process. In conclusion, the mid-Neoproterozoic transitional subduction has resulted in the distributed deep Pre-Sinian rifts in the Sichuan Basin, which is a new favorable hydrocarbon exploration frontier.