The river originates in a glacier lying on the west of Geladandong Mountain in the Dangla Mountain Range on the eastern part of the Tibetan plateau. It runs eastward through Qinghai, turning southward down a deep valley at the border of Sichuan and Tibet to reach Yunnan. In the course of this valley, the river's elevation drops from above 5000 m to less than 1000 m. The headwaters of the Yangtze are situated at an elevation of about 4,900 m (16,000 ft). In its descent to sea level, the river falls to Chongqing. Between Chongqing and Yichang, at an altitude of 40 m (130 ft) and a distance of about 320 km (200 mi), it passes through the spectacular Yangtze Gorges, which are noted for their natural beauty.

The Yangtze flows into the East China Sea and was navigable by ocean-going vessels up to a thousand miles from its mouth even before the Three Gorges Dam was built. As of June 2003, this dam spans the river, flooding Fengjie, the first of a number of towns affected by the massive flood control and power generation project. This is the largest comprehensive irrigation project in the world and has a significant impact on China's agriculture. Its proponents argue that it will free people living along the river from floods that have repeatedly threatened them in the past and will offer them electricity and water transport—though at the expense of permanently flooding many existing towns (including numerous ancient cultural relics).

The river is one of the world's busiest waterways. Traffic includes commercial traffic transporting bulk goods such as coal as well as manufactured goods and passengers. Cargo transportation reached 795 million tons in 2005. River cruises several days long, especially through the beautiful and scenic Three Gorges area, are becoming popular as the tourism industry grows in China.