Megalophthalma is distinguished from other temnospondyls by its very large orbits or eye sockets, which occupy most of the skull and are bordered by thin struts of bone.

In fact, Megalophthalma and Plagiosternum are thought to form their own clade or evolutionary grouping within Plagiosauridae called Plagiosterninae.

In overall form Megalophthalma and Plagiosternum are intermediate between the basal plagiosaurid Plagiosuchus (which more closely resembles non-plagiosaurid temnospondyls) and the derived Gerrothorax (which has an even more highly modified skull than plagiosternines).

The eye was probably positioned near the front of the orbit as in modern small-eyed amphibians like cryptobranchid salamanders and pipid frogs.

Another possibility, although far less likely, is that Megalophthalma and other plagiosaurids had eyes similar to those of the living deep-sea fish Ipnops, which are reduced to sheet-like retina that cover the upper surface of the skull and are only able to detect movement from shadows.