River-controlled permafrost dynamics are crucial for sediment transport, infrastructure stability, and carbon cycle, yet are not well understood under climate change. Leveraging remotely sensed datasets, in-situ hydrological observations, and physics-based models, we reveal overall warming and widening rivers across the Tibetan Plateau in recent decades, driving accelerated sub-river permafrost thaw. River temperature of a representative section (Tuotuohe River) on the central Tibetan Plateau, has increased notably (0.39 degrees C/decade) from 1985 to 2017, facilitating heat transfer into the underlying permafrost via both convection and conduction. Consequently, the permafrost beneath rivers warms faster (0.37 degrees C-0.66 degrees C/decade) and has a similar to 0.5 m thicker active layer than non-inundated permafrost (0.17 degrees C-0.49 degrees C/decade). With increasing river discharge, the inundated area expands laterally along the riverbed (16.4 m/decade), further accelerating permafrost thaw for previously non-inundated bars. Under future warmer and wetter climate, the anticipated intensification of sub-river permafrost degradation will pose risks to riverine infrastructure and amplify permafrost carbon release.