Its fossils have been found at the Ringtail Site in the Riversleigh World Heritage Area (north-western Queensland) and date to the Miocene epoch.

Like the closely related Mekosuchus, it is thought to have had a short and blunt snout and large eyes that generally resembles today's dwarf crocodiles.

Most material of this genus has been collected from the middle Miocene Ringtail Site of the in Riversleigh, one of Australia's most famous fossil localities.

[1] The holotype skull was uncovered in 1985 during an excavation by the University of New South Wales and is currently considered to be among the best preserved fossil crocodilians from Australia, in spite of the missing snout.

The genus Trilophosuchus was erected in 1993 with the description of the remains by Paul Willis of the University of New South Wales in the Journal of Vertebrate Paleontology.

[1][4] The name Trilophosuchus derives from Ancient Greek and translates to "triple-crested crocodile", referring to the three parallel ridges that run along the animal's skull table.

[2][1] The most distinct feature of Trilophosuchus, and the one that gives this taxon its name, is the presence of three prominent crests that extend alongside the length of the crocodilian's skull table.

Two additional crests run parallel to this medial ridge, originating at the orbital margin and stretching from there until the end of the skull table, occupying the space between the midline and the fenestrae.

Willis also notes the presence of small knobs on the outer side of the skull table, separated from the three ridges by the supratemporal fenestrae.

However, between the sixth and seventh alveoli this even spacing is interrupted by a dentary tooth of the lower jaw that interlocks with the upper dentition and creates a prominent notch in the maxilla.

[2] Based on the known remains, Trilophosuchus shows a high degree of festooning, meaning the maxillae are distinctly wave-like in their form, visible in both side and top view.

[4] The inner ear features a distinctly sub-triangular vestibular apparatus (where the semicircular canals contact the common crus), as opposed to being more rounded like in other modern crocodilians.

They further point out that although the compression of the supratemporal fenestrae is a juvenile trait, their orientation does not match this interpretation, while the inclination of the occipital face could also be explained as being the ancestral condition.

[4] The skull of Trilophosuchus only measures 79 mm (3.1 in) from the back of the head to the front most preserved part of the rostrum, making it very small even when accounting for the missing material.

While research on Australian crocodilians was still in its early days during the time of Trilophosuchus description, it was already recognized that it formed a monophyletic clade with the genera Quinkana, Pallimnarchus, Baru and Australosuchus.

[2] Additional studies and new discoveries in subsequent years led to a better understanding of the group, eventually dubbed Mekosuchinae following the inclusion of Mekosuchus from New Caledonia and Australia.

[3] Mead et al. (2002) also recovered such a clade, but placed Trilophosuchus as the basalmost genus in it, outside of the group formed by Quinkana, Mekosuchus and Volia (which had not been named at that point in time).

In their research, morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data once again showed support for Trilophosuchus being part of an altirostral clade including Volia, Mekosuchus and Quinkana, only differing slightly in the internal relationships of this grouping.

[5] The re-evaluation of Ultrastenos and "Baru" huberi eventually came to lend credence to the tree previously published by Stein et al. in 2016, as the results indicate that "Baru" huberi and Ultrastenos were the same taxon and the sister to the clade that includes Trilophosuchus, Mekosuchus and Volia while maintaining an overall topology similar to that of Ristevski et al.

The inclination of the posterior skull and the neck musculature indicates that this genus held its head higher above the body than most modern taxa, with Willis comparing it to basking caimans and agamid lizards.

However, as this muscle is only poorly developed in Trilophosuchus, the animal likely didn't have to deal with the same resistances as today's crocs and subsequently needed less power to begin shaking its head.

Instead, Willis looked to older forms like notosuchians and protosuchids, which are generally considered to be terrestrial animals based on not only their skulls but also their limb proportions.

[2] Willis also compares Trilophosuchus to Boverisuchus and Sebecus, two terrestrial crocodylomorphs from the early Cenozoic, noting major differences in the shape of the rostrum.

While the latter have deeper and more elongated jaws and grow notably larger, Trilophosuchus was small with a boxy skull, a sign that it did not inhabit the same niche even if it was terrestrial.

Several researchers for instance have previously found a correlation between the cranial pneumaticity and aspects of the respective animal's lifestyle, which is briefly discussed by Ristevski and colleagues while describing the neuroanatomy of Trilophosuchus.

The overall shape of the endocast has been compared most closely to the terrestrial notosuchian Araripesuchus, while the ratios between the elements of the inner ear shows similarities to some baurusuchids and sphenosuchians among others.

For instance, the Ringtail Site also preserves the bones of Baru, a large semi-aquatic ambush predator that is unlikely to have competed for the same resources as the much smaller Trilophosuchus.