<p>The initial timing of uplift at the southeastern margin of the Tibetan Plateau (SMTP) remains under debate, with estimates ranging from the Eocene, to the Oligocene. The Jinsha River was formed before the Miocene, therefore, it is likely to record the uplift information of the Tibetan Plateau, which is important for understanding the tectonic uplift of the SMTP. Here, we collected granite samples from the Yangla area in the middle part of the Jinsha River, and analyzed the uplift characteristics of the Cenozoic in the middle part of the Jinsha River by using the apatite fission tracks and the river longitudinal profiles. We show that the uplift time of the first phase is about 25–20 Ma, and the uplift time of the second phase is about 5 Ma. From the channel profile, seven tributaries of the Jinsha Rivers also have developed two phases of knickpoints. The tributaries consist of three sections with distinct geomorphological parameters, each separated by knickpoints. We argue that large-scale uplift occurred in the Late Cenozoic on the SMTP, with different locations having different uplift times, and the interior may have undergone significant uplift in the early Oligocene, but significant uplift of the SMTP occurred by the Late Oligocene to Early Miocene. The Jinsha River flowing from the interior of the plateau has developed multiple knick points during the uplift process, recording information about the uplift of the Tibetan Plateau.</p>