The skull in all known specimens is poorly preserved, but in general appears to have had a narrow snout compared to the closely related "Longicrusavis". The teeth were very small and are poorly preserved in all known specimens. At first, this led scientists to conclude that the teeth were absent in both the upper and lower jaws, probably replaced with a beak. However, later study of the type specimen showed that tooth sockets were present in the preserved parts of the jaw, and comparison with related forms showed that it did have teeth. The discovery of a more well preserved specimen confirmed the presence of teeth in at least the maxilla (middle of the upper jaw) and dentary (lower jaw). The snout appears to have lacked feathers, though whether it was only covered in skin or some parts bore a beak is currently unknown. The describers of "Hongshanornis" noted a unique bone in the end of the lower jaw which they equated with the beak-bearing "predentary bone" similar to the one found in ornithischian dinosaurs. Such bones have also been found in more advanced birds like "Hesperornis". However, other scientists have pointed out that the "predentary" (or, technically, "mandibular symphysial ossification") of "Hongshanornis" lacks the characteristic pits and grooves associated with the beak in early beaked birds like "Archaeorhynchus", and that the presence or absence of any beak is unclear.