The county has a total area of 473.36 square miles, of which 471.52 square miles (99.61%) is land and 1.84 square miles (0.39%) is water.

Much of Madison County rests on top of a shield volcano just north of Rigby, ID. Eruptions are not expected in the near future this far south; besides Yellowstone Park is the most likely setting for future volcanic activity in this area. Many different types of volcanoes exist near Madison County, including cinder cones, spatter cones, other shield volcanoes, and volcanic fissures. There are lava fields to the west and south, the results of open fissure eruptions from about two thousand years ago. Nearby Craters of the Moon National Monument presents the most obvious features of this recent activity. Sediment deposits enriched by volcanism make the surrounding area famous for its production of large starch-rich potatoes.

Madison County is close to the St. Anthony Sand Dunes, the West Entrance of Yellowstone National Park and the Teton Range.

Adjacent counties  
Unincorporated Communities & Townships National protected areas Highways