The Afar region presents a unique example of a juvenile R‐R‐R triple junction with the arms evolved to various stages of maturity. The lithosphere in this area has been modified heterogeneously by the nearby Afar mantle plume. To gain a comprehensive and consistent understanding of the link between crustal geometry and geodynamics of the region and facilitate comparisons across different tectonic elements, we developed a high‐resolution crustal thickness map of the region that resolves major tectonic features. The calculation involved a well‐constrained 3‐D inversion of upper mantle‐corrected crustal Bouguer gravity anomalies computed with the help of tomography‐derived densities. Our results match earlier localized crustal thickness estimates, illustrating the method's efficacy. A thinner crust (∼20–26 km) is revealed in the Afar compared to adjacent continental regions. The Main Ethiopian Rift has the thickest crust in the central part of the rift (∼38–40 km) and thinner to the north (∼30 km) and south (∼35 km). The crustal thickness along the Gulf of Aden changes from east (∼5 km) to west (∼17 km) in the west, consistent with a westward transition from seafloor spreading to continental rifting. The southern Red Sea is characterized by asymmetric crustal thickness, with a thicker crust (∼17 km) on the eastern flank compared to the western flank (∼11 km), which we attribute to the influence of a sub‐lithospheric channel from the Afar mantle plume. We propose a model describing the channel leading to asymmetric features of the southern Red Sea, such as crustal accretion, marginal topography, and volcanism.