Shigatse-Jilong Railway is located on the tectonic boundary zone of plate collision in southern Tibet, Across the three major Quaternary active rifts of Dingjie, Gangga and Peikucuo. The active faults distributed in each rift valley have an important influence on railway route selection and engineering design. Through field investigation and testing of 25 faults in each rift valley along the Shigatse-Jilong Railway, It is found that the project crosses 10 late Pleistocene active faults, including 4 Holocene active faults, including Dingjie fault, Guojia fault, dengmoduo fault in Dingjie riftand gangpengqing fault in peikucuo rift. For Dingjie fault and Guojia fault, The south section with relatively weak activity can be selected to pass through with simple works, For dengmoduo fault with the strongest Holocene activity along the whole line, it is suggested to pass through in the form of subgrade. Due to the high risk of future earthquakes, gangpengqing fault zone should avoid passing through tunnel engineering.