Istiodactylus was quite a large pterosaur, with estimates of its wingspan ranging from 4.3 to 5 metres (14 to 16 ft). This makes it the largest known member of its family, Istiodactylidae. Some isolated pterosaur wing-bone fragments that may belong to this genus indicate a wingspan as large as 8 metres (26 ft). The most completely known skull is fragmentary but is thought to have been about 45 centimetres (18 in) in length, based on a long-lost fragment of its jaw reported in 2012. Before this, the skull had been estimated to be 56 centimetres (22 in) long. At 28.5 centimetres (11.2 in), the jaws were less than 80 percent of the skull's length, which is short for a pterodactyloid pterosaur. As a pterosaur, Istiodactylus would have been covered in hair-like pycnofibres, and had extensive wing-membranes, which were distended by a long wing-finger.
The skull of Istiodactylus was relatively short and broad compared to most other pterosaurs, and it had a short, low snout-region in front of the nostrils. Much of the skull was occupied by very large naso-antorbital fenestrae (openings which combine the antorbital fenestra and the bony nostril). Unusually, this opening extended past the jaw joint and the back of the mandible. The orbit (eye socket) was reclined and slender, and was capped at the front by a tuberosity. The hind part of the skull was relatively tall, and the skull table bore a low crest or ridge at the front. The mandibular symphysis was abbreviated, and the mandible was deepest where the mandibular rami (halves of the lower jaw) diverged. The maxilla of the upper jaw was very slender, and only 6–7 millimetres (0.2–0.3 in) deep. The tip of the beak was rounded, blunt, and heavily built.
The tips of the jaws bore a semicircle of 48 teeth which were even in size, triangular, and compressed sideways. The teeth have been described as "petal-like" or "lancet-like". The teeth had sharply pointed crowns and triangular roots that were shorter than the crowns. Most tooth crowns had slightly blunted points, or were somewhat worn. The margins of the tooth crowns were not serrated, but had faint keels. There were 24 upper teeth, restricted to the part in front of the nostril, and 24 lower teeth, restricted to the symphysal region. The upper and lower teeth interlocked, forming a "razor-edged" or "zig-zag" outline. The front teeth were closely spaced, and the hind teeth were more widely spaced, with recesses for the opposing teeth. A sharp projection between two teeth at the middle front of the mandible has been described as an odontoid (or "pseudo-tooth"), but was previously interpreted as an actual tooth. The odontoid may have been encased in a keratinous covering so that it could occlude with the teeth.
Apart from the skull, the skeleton of Istiodactylus was similar to those of other ornithocheiroid pterosaurs. The vertebral column, forelimb, and trunk bones were pneumatised by air sacs. The neural arches of the vertebrae had tall, sloping laminae. The notarium (a structure consisting of fused vertebrae in the shoulder-region of some pterosaurs and birds) consisted of six fused trunk vertebrae, with their neural spines fused into a plate, on which the shoulder blades articulated with a depression on each side. The main part of the sternum was very deep, with a bowed front edge and a shallow, triangular keel. The facets of the sternum that contacted with the coracoids were saddle-shaped and arranged asymmetrically. The humerus (upper arm bone) was stout and had a sharply curved deltopectoral crest. The forelimbs of istiodactylids were large, up to 4.5 times longer than their legs. The long wing-finger may have occupied 50 percent of the wing-skeleton. The hindlimbs were short compared to the forelimbs, and the feet were as long as the small third finger.