East Turkestan covers an area of 1.82 million square kilometers, which is twice as large as the Republic of Turkey or four times as large as the American state of California. More than 43 percent of East Turkestan is covered by deserts and another 40 percent is covered by mountain ranges.

The main characteristic of this huge land is two basins bounded by three mountain ranges. The two basins are Tarim basin in the south, which is 530,000 square kilometer, and the Junggar basin in the north, which covers an area of 304.200 square kilometers. Tarim basin contains one of the largest deserts in the world—the Taklamakan desert. The Junggar basin contains the Kurbantunggut desert.

Tengritagh mountain (Heavenly mountain) crosses the central part of East Turkestan dividing the country into south and north. Within East Turkestan, the Tengritagh mountain is 1700 kilometers long and 250-300 kilometers wide. Altay mountain in north forms the border of East Turkestan, Mongolia, Russia and Kazakhstan. Its section within East Turkestan is 400 kilometers. The Kunlun mountain is the south is the border between East Turkestan and Tibet.

The most important rivers are the Tarim river (2137 km long), flowing almost the whole length of southern part of East Turkestan and empties into desert; the Ili river, flows west into the Kazakhstan and eventually flows into Lake Balqash; the Irtish river flows northwest out of East Turkestan into the Arctic Ocean; the Karashaar river, flows east from central Tengritagh into Lake Baghrash; the Konche river, starting from the Baghrash lake, originally flows into Lopnur Lake, but now disappears in the desert long before reaching the lake.