Middle Paxton Township is in central and western Dauphin County, bordered to the southwest and west by the Susquehanna River. The township is in the Ridge and Valley Province of the Appalachian Mountains; four parallel mountain ridges cross the township from southwest to northeast. The northern border of the township follows the crest of Peters Mountain. Next to the south is Third Mountain, followed by Second Mountain, which forms part of the southern border of the township, and finally Blue Mountain, which forms the remainder of the southern border.