Like the other large river systems that drain the area of the India-Asia collision, the Yangtze River was assembled through a series of Cenozoic capture events. These events are important for orogenic erosion and sediment delivery, but their timing remains largely unknown. Here we identify enhanced cooling in the Three Gorges region in central China, a key capture site during basin development, beginning at 40–45 Ma. This event is not visible in regional thermochronological data, but is near-contemporaneous with the onset of widespread denudation in the Sichuan Basin, just upstream of the Three Gorges. While we cannot rule out alternative explanations, the simplest mechanism that links these events is progressive capture of the middle Yangtze River by the lower Yangtze and the onset of incision in the Three Gorges. This model agrees with independent mid-Cenozoic estimates for the timing of middle Yangtze River diversion and capture, and provides a plausible outlet for large volumes of erosional detritus from the Sichuan Basin.