[3] Mesohippus had longer legs than its predecessor Eohippus and stood about 60 cm (6 hands) tall.

This equid is the first fully tridactyl horse in the evolutionary record, with the third digit being longer and larger than its second and fourth digits; Mesohippus had not developed a hoof at this point, rather it still had pads as seen in Hyracotherium and Orohippus.

The eyes were rounder, and were set wider apart and further back than in Hyracotherium.

Unlike earlier horses, its teeth were low crowned and contained a single gap behind the front teeth, where the bit now rests in the modern horse.

[5] The cerebral hemisphere, or cranial cavity, was notably larger than that of its predecessors and its brain was similar to modern horses.