Thiksey is located in the Indus River Valley, deep within the Trans-Himalayan region. The physical geography is defined by a high-altitude cold desert environment. The village itself rests on a relatively flat and fertile flood plain alongside the Indus River, bordered by the soaring, barren peaks of the Stok Range to the south and the Ladakh Range to the north.
The terrain is stark and rugged, characterized by rocky outcrops, scree slopes, and deep valleys. Because the region lies in the rain shadow of the Great Himalayas, it receives very little monsoon rain, resulting in an arid landscape. The vivid green of Thiksey's agricultural fields—nourished by glacial meltwater and the river—creates a striking visual contrast against the ochre and purple hues of the surrounding desert mountains. Natural resources primarily consist of the vital freshwater streams (tokpos) and abundant solar energy.