As a typical orogenic gold deposit in Tibet, Shangxu gold deposit is located at the Bangong Lake–Nujiang River Metallogenic Belt in the south of Qinghai–Tibet Plateau. In this paper, zircon U-Pb dating, trace elements and Hf isotopic analysis were performed on Au-bearing quartz veins in the Shangxu gold deposit. Zircons from Au-bearing quartz veins can be divided into three types: detrital, magmatic, and hydrothermal zircons. There are two age peaks in detrital zircons: ca. 1700 Ma and ca. 2400 Ma. There are two groups of concordant ages including 157 ± 4 Ma (MSWD = 0.69) and 120 ± 1 Ma (MSWD = 0.19) in magmatic zircons, in which εHf(t) value of ca. 120 Ma from the magmatic zircons range from +8.24 to +12.9. An age of 119 ± 2 Ma (MSWD = 0.42) was yielded from hydrothermal zircons, and their εHf(t) values vary between +15.7 and +16.4. According to sericite Ar-Ar age, this paper suggests that an age of 119 ± 2 Ma from hydrothermal zircons represent the formation age of the Shangxu gold Deposit, and its mineralization should be related to the collision between Lhasa Block and Qiangtang Block. The metallogenic age is basically the same as the diagenetic age of Mugagangri granite, and εHf(t) value of hydrothermal zircon is significantly higher than that of the contemporaneous magmatic zircon, which indicates that there is a genetic relationship between the gold mineralization and the deep crust-mantle magmatism.