The jaws of Nyctosaurus were long and extremely pointed. The jaw tips were thin and needle sharp, and are often broken off in fossil specimens, giving the appearance that one jaw is longer than the other, though in life they were probably equal in length.

 Nyctosaurus is the only pterosaur to have lost its clawed "fingers", with the exception of the wing finger (of which however the fourth phalanx was lost), which is likely to have impaired its movement on the ground, leading scientists to conjecture that it spent almost all of its time on the wing and rarely landed. In particular, the lack of claws with which to grip surfaces would have made climbing or clinging to cliffs and tree trunks impossible for Nyctosaurus.

 A few scientists had initially hypothesized that this crest, which resembles an enormous antler, may have supported a skin "headsail" used for stability in flight. While there is no fossil evidence for such a sail, studies have shown that a membranous attachment to the bony crest would have imparted aerodynamic advantages. However, in the actual description of the fossils, paleontologist Christopher Bennett argued against the possibility of a membrane or soft tissue extension to the crest. Bennett noted that the edges of each prong were smooth and rounded, and showed no evidence for any soft-tissue attachment points. He also compared Nyctosaurus with large-crested tapejarids, which do preserve soft tissue extensions supported by prongs, and showed that in those species, the attachment points were obvious, with jagged edges where the transition from bone to soft tissue occurred. Bennett concluded that the crest was most likely used solely for display, citing similar structures in modern animals. The 2009 study by Xing and colleagues testing the aerodynamics of the giant crest with a "headsail" also tested the aerodynamics of the same crest with no sail, and found that it added no significant negative factors, so a crest with no headsail would not have hindered normal flight. It is more likely that the crest acted mainly for display, and that any aerodynamic effects it may have had were secondary. Bennett also argued that the crest was probably not a sexually dimorphic character, as in most crested pterosaurs, including the related Pteranodon, both sexes are crested and it is only the size and shape of the crest that differs. The apparently non-crested Nyctosaurus specimens therefore probably came from sub-adults.

 The ecosystem preserved in this zone was unique in its abundance of vertebrate life. Nyctosaurus shared the sky with the bird Ichthyornis and with Pteranodon longiceps, though the second Niobrara Pteranodon species, P. sternbergi, had disappeared from the fossil record by this point. In the waters of the Western Interior Seaway below swam mosasaurs (Clidastes, Ectenosaurus and Tylosaurus), the flightless diving bird Parahesperornis, and a wide variety of fish, including swordfish-like Protosphyraena, the predatory Xiphactinus and the shark Cretolamna.