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Located on the north wing of the Yangtze River estuary, Nantong is in the southeastern part of Jiangsu province, adjacent to Taizhou to the west, and bordering on Yancheng to the north. Nantong is surrounded by water on three sides, and thus is shaped as a peninsula, with its northern to the northeastern parts adjacent to the Huanghai Sea, and its southern part facing the Yangtze River. Nantong is connected to Suzhou and Shanghai via two cross-river bridges, the Su-Tong Yangtze River Highway Bridge and the Chongqi Bridge.

The city covers a total area of 8,001 square kilometers, 1,521 of which are urbanized. The river and sea lines are 425 kilometers in length, and include 219 kilometers of the Yangtze River bank line and 206 kilometers of coastline.