It is widely accepted that tectonics generally enhances river incision. However, the question as to why on a global-scale, rivers have not incised further into orogenic plateaus to destroy terrains over long-timescales remains ambiguous. Here we hypothesize that the diverse nature of regional tectonics could have impeded river erosion to maintain plateau topography, taking Yarlung River in Tibetan Plateau as a case. We constrain the incision history and effect of a tectonic rift on the evolution of fluvial incision by the low-temperature thermochronology. Results show fast cooling since ~7 Ma focused near the rift, but markedly reduced cooling in the upstream and downstream regions. This indicates that the steep flank fault of the rift controlled local rapid exhumation as a knickpoint since that time. This coincides with an episode of rapid exhumation of Eastern Himalaya Syntaxis (EHS) downstream. We propose that these two co-phased tectonic systems resulting from accelerated late Miocene extension of southern Tibet, along with downstream stabilization of base levels at EHS, prevented upstream migration of river knickpoints, and impeded fluvial incision. Our study highlights that the activity of fault systems may hinder regional erosion, thereby facilitating the preservation of topography and high plateaus in active orogenic belts.