The topography of Mokokchung is quintessentially hilly. The municipal area is spread across a series of interconnected ridges and slopes, with an average elevation of approximately 1,325 meters (4,347 feet) above sea level.
The city does not feature flat plains; instead, urban development has been adapted to the contours of the land, resulting in terraced housing and winding roads. The highest points in the immediate vicinity provide vantage points over the steep ravines and valleys that characterize the district's landscape. The Dikhu river valley forms a significant topographical feature to the east, while the western slopes gradually step down toward the borders of Assam.

