Koh Samui is in the Gulf of Thailand, about 35 km northeast of Surat Thani town (9°N, 100°E). It is the most significant island in the Chumphon Archipelago. The island measures some 25 km at its widest point. To the north are the populated resort islands of Koh Pha-ngan, Koh Tao, and Koh Nang Yuan.

Close to Bangrak in northeast Samui is the small uninhabited island of Koh Som, and to the northeast of Chaweng is the tiny Koh Matlang. To the south are Koh Taen and Koh Matsum, each of which have small tourist facilities. To the far west are 44 other islands which together compose Mu Koh Ang Thong National Park which is accessible by a day-trip boat tour from Koh Samui.

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The central part of Koh Samui is mostly tropical jungle, including its largest mountain, Khao Pom, peaking at 635 meters. The various lowland and coastal areas are connected by Route 4169, which is a 51 kilometer–long road, encircling the island. Many other concrete roads branch out from Route 4169 to service other areas.

On the west coast of the island is the original capital, Nathon, which still houses many government offices, as well as two of the island's five major piers. Nathon is the major port for fisheries and for vehicular and goods transportation from the mainland. As the site of the main port and the closest city to the mainland has made Nathon the commercial center for Samui locals. More recently, the transition from dependence on the local coconut industry along with the continued growth and development of the tourist industry, as well as the northeastern location of the airport, has led to the increase of commercial activity in Chaweng and Bophut.