Abstract: In this paper, the characteristics of major and trace elements of chert from southern Tibet are studied by the way of factor analysis, and the first, second and third factors are concluded from the results. It is showed that from Pengcuolin, Xialu to Zongzhuo chert profile, the variance ratios of continental and authigenetic factors become higher, while hydrothermal factor rapidly decrease, which indicate that Pengcuolin chert is originated from hydrothermal deposit, while Zongzhuo chert is derived from normal sedimentation and the genesis of Xialu chert is caused by integrated action of the hydrothermal deposit and normal deposit.