Khonsa is situated in the southeastern part of Arunachal Pradesh, perched within the rugged terrains of the Eastern Himalayas. The geography is characterized by dense, evergreen, and semi-evergreen sub-tropical forests that carpet the rolling hills and deep valleys. The town lies near the international border with Myanmar to the east and south, and the Indian states of Assam and Nagaland to the north and west.
The natural environment around Khonsa is rich in biodiversity, hosting a variety of rare orchids, medicinal plants, and wildlife, including leopards, wild boars, and various species of hornbills. Rivers and mountain streams—most notably the Tirap River—carve through the landscape, serving as crucial water sources for the valleys below. The soil here is primarily lateritic and forest soil, which supports traditional hill agriculture.