The Carthax sector covers a large spatial area and is therefore divided into a number of sub-sectors. Although each sub-sector is generally self-governed, overall administration of the sector is carried out from Pillarus Prime. Sector government comprises a senate headed by the Imperial Governor and including representatives from the various Adeptus, representatives of the various sub-sector governments, and prominent trade bodies.
- The Al-Gheri sub-sector - Large sub-sector at Eastern border of Sector. Oldest region of Carthaxian space.
- The Avaris corridor - A small centrally located sub-sector, concealed from most of Carthax by a combination of massive interstellar dust clouds and severe warpstorms. The only known safe route inwards is Ariepate's Path.
- The Cuir sub-sector - Located to the north-east of the main Carthax sector, this region was discovered in the Nakt Crusade of late M32, and is officially considered part of the Carthax sector.
- The Valmerine sub-sector - a cluster of systems towards the Carthax Sector's spinward boundary, bordering the Atrean Gulf.
Within the sub-sectors are a number of spatial regions that are known of across the sector. These areas represent astronomical locales, quite often isolated by channels through the warp. While thought of as part of a greater whole, some of these these regions may receive sub-sector designation in their own right once more Imperial control is devolved to their locales.
- The Antonine cluster - a star cluster to the spinward edge of the Cuir sub-sector. The Cold Trade in xenos artefacts is centred here.
- Bassit's Gulf - a narrow and long region that snakes around between the five others that make up the Al-Gheri sub-sector. Its capital system Avoniaz is both a major trading hub and "second home" to the Imperial Navy in the Sector due to its incredibly stable warp routes to many of the other sub-sectors.
- Dioklesian nebula - A stellar remnant on the border between the Al-Gheri and Cuir sub-sectors. Originally investigated as a source of rare elements, but now accepted as one of the most dangerous warp hazards in the sector.
- Far Carthax - the western most region of the Al-Gheri sub-sector, bordering The Wilderwest. Unfavourable warp conditions make travel difficult and there are a number of uncharted systems yet to be catalogued by the Explorator Fleets.
- The Gaugtel stars - a region of unexplored space on the edge of the Carthax Sector. No ship entering the region has ever returned.
- Greater Pillarus Core - the commercial and political hub of the sector, residing in the north of the Al-Gheri sub-sector. Home to sector capital, Pillarus Prime.
- Hydronus Landing - the first systems conquered by House Hydronus on the sector's discovery, including the first sector capital, Carthage. Hydronus Landing is now considered part of the Al-Gheri sub-sector.
- Lesser Pillarus Core - a small and sparsely populated region of the Al-Gheri sub-sector.
- The Onus region - Vast tract of inhospitable systems on the southern fringe of the sector, famed for its still-bountiful raw mineral deposits and unforgiving climates.
- Prastian Straits - a region on the southern edge of the sector renowned for difficult warp navigation, and the sector's most populous system, Colossus.
- The Wilderwest - the most western point of the Carthax sector, extending beyond the light of the Astronomicon and into the Halo stars.