The urban center is in the northwest, where there is flat land at the southern end of the Kumamoto Basin, but nearly 80% of remaining area of the town is mountainous and forested.

Kumamoto Prefecture Misato has a humid subtropical climate (Köppen Cfa) characterized by warm summers and cool winters with light to no snowfall.

After the Meiji restoration, the villages of Nakayama, Nishine, Nishitomochi and Higashitomochi were established with the creation of the modern municipalities system on April 1, 1889.

Misato has a mayor-council form of government with a directly elected mayor and a unicameral town council of 10 members.

In terms of national politics, the town is part of the Kumamoto 4th district of the lower house of the Diet of Japan.