The phylogenetic relationships within crown Crocodylia remain debated due to conflicts between molecular and morphological hypotheses. Morphology-based datasets are historically constructed on external characters, overlooking internal structures despite the disparity observed in the neuroanatomy and pneumaticity of crocodylians. Additionally, taxonomical determinations are still difficult based on cranial characters only, notably in the genus Crocodylus. Investigating endocranial anatomy is thus needed to develop a better picture of crocodylian anatomy and evolution. Here, we present a 3D geometric morphometric study of the crown group, which focuses on the development of the intertympanic diverticula in a large dataset of extant and subfossil crocodylian specimens. The intertympanic diverticula, a pneumatic space located above the brain and between the middle ears, displays a specific morphology that changes during ontogeny and differs among taxonomic groups. We find that all hatchlings share the same sinus morphology, and that intertympanic diverticula growth is modulated by cranial shape, especially in longirostrine species. Still, developmental patterns were found to distinguish specimens at the family and genus rank. We show a clear distinction between Alligatoridae and Longirostres, as well as between Tomistoma and Gavialis lineages. Crocodylus species are also distinguished, showing different morphologies associated with biogeographic clusters. This approach is independent of molecular methods but mainly concurs with the molecular topologies. Therefore, the investigation of crocodylian sinus anatomy may promise major advances for the phylogenetic study of fossil specimens, pending more information on the precise ecological roles of these internal structures.