The skull of Sphenacodon is very similar to that of Dimetrodon. It is narrow from side to side and vertically deep, with an indented notch at the front of the maxillary bone in the upper jaw. The upper and lower jaws are equipped with an array of powerful teeth, divided into sharp pointed “incisors”, large stabbing “canines”, and smaller slicing back teeth. The orbit is set high and far back with a single opening (temporal fenestra) behind and partly below the eye, a characteristic of synapsids.
Body proportions are also similar to Dimetrodon, with a very large head, short neck, robust trunk, relatively short front and hind limbs, and a tapering tail that makes up about half the animal’s entire length. However, the tops of the neural spines along the back bone are strikingly different in each genus. In Dimetrodon, the neural spines develop into long, narrow, cylindrical projections that support a tall vertical dorsal sail that ends near the base of the tail. In Sphenacodon, the neural spines are enlarged but retain a flat-tipped, blade-like shape along the back and tail, and form a crest rather than a tall sail. (The sphenacodontid genus Ctenospondylus also has blade-like neural spines, but its dorsal crest is taller than in Sphenacodon, although not as tall as the sail in Dimetrodon.)
There is evidence for strong epaxial muscles along the base of the raised neural spines in both Sphenacodon and Dimetrodon, likely helping to stiffen and strengthen the backbone for walking and for lunging at prey by restricting side-to-side flexing motion. A recent study of the structure of the neural spines on Sphenacodon confirms that the upper parts were not encased in a thick muscular hump and instead protruded above a layer of muscle to form a low dorsal crest. Finds of sphenacodontid specimens in which postmortem distortion of the body caused the dorsal spines to overlap suggests that the spines were not connected by hard or particularly tough tissue. The possible function of a low, skin-covered crest in Sphenacodon is debated. A thermoregulatory role seems unlikely, although the taller crest in Sphenacodon ferocior is allometrically larger than in S. ferox. Recent research has favored a display role for the tall sails in Dimetrodon and Edaphosaurus.
Both Sphenacodon and Dimetrodon have been depicted with their short limbs splayed outward at 90 degrees from the body in a wide pushup position and with the tail (and even belly) dragging on the ground, similar to modern lizards and crocodiles. A sprawling stance is also typical for Sphenacodon and Dimetrodon skeletons as currently mounted in museums. However, trackways called Dimetropus (“Dimetrodon foot”) that match the foot configuration of large sphenacodontids show animals walking with their limbs brought under the body for a narrow, semi-erect gait without tail or belly drag marks. Such clear evidence for a more efficient upright posture suggests that important details about the anatomy and locomotion of Sphenacodon and Dimetrodon may not be fully understood. Some well preserved narrow Dimetropus tracks found in parts of the Prehistoric Trackways National Monument in New Mexico match the smaller size of Sphenacodon, a genus known from skeletal fossils in the state, but could also come from a small Dimetrodon.