Nagayo is located on the southern shore of Ōmura Bay in central Nagasaki Prefecture, and includes the uninhabited islands of Shimizu and Futatsujima.

The surrounding areas are hilly, and especially on the eastern side, there are a series of hills centered on Kotonoodake, which is 451.4 meters above sea level.

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

In terms of national politics, the city is part of the Nagasaki 2nd district of the lower house of the Diet of Japan.

The local economy was formerly centered on agriculture and commercial fishing; however, Nagayo is now largely a commuter town for Nagasaki.