The Hercynian Orogeny was caused by the collision of Gondwana and Laurussia in the Mid‐/Late Carboniferous–Early Permian. This orogeny strongly influenced the pattern and evolution of basins and hydrocarbon accumulation on the southern margin of the Tethyan region (i.e., North Africa and the Middle East). Research on the Carboniferous–Early Permian Hercynian Orogeny is of great value in both plate tectonic reconstructions and hydrocarbon exploration. For its influence on basin evolution, some previous studies have considered the modification of the early Palaeozoic basins, but there has been less work on the evolution of the post‐Hercynian Mesozoic basins. We review the available data and re‐analyse the spatiotemporal impacts of this key tectonic event on the evolution of the basins in this region. The Carboniferous–Early Permian Hercynian Orogeny was an important turning point in basin evolution in North Africa and the Middle East. It interrupted the stability of the Gondwana platform and heralded a huge change in the pattern of basins from the uniform pre‐Hercynian Palaeozoic basins to the post‐Hercynian Mesozoic basins characterized by strong segmentation. The Carboniferous–Early Permian Hercynian Orogeny not only modified the pre‐Hercynian Palaeozoic basins but also controlled the distribution and evolution of the post‐Hercynian Mesozoic basins. Large‐scale uplifts were generated among the basins through modification of the inherited palaeohighs and five large NE‐trending arches were newly formed. These uplifts divided the early unified basin into multiple separate basins. Five large‐scale, almost equidistant, NE‐trending arches were generated on the northern margin of Gondwana (the Allala, Sirte, Levant, Al‐Batin and Oman arches), forming the present‐day Palaeozoic Basin pattern with an alternating distribution of uplifts and depressions. The northern part of the large, NE‐trending Hercynian arches collapsed as a result of the extensional stress caused by the opening of the Neotethys Ocean in the Late Permian–Triassic and formed Mesozoic basin depocenters (the Oued Mya–Pelagian basins, the Sirte Basin, the Eastern Mediterranean Basin and the Central Arabian Basin). These depocenters are important oil and gas enrichment zones. The NE‐trending Hercynian arches, the Mesozoic basin depocenters, the opening of the Neotethys Ocean and the segmentation of the basins by the Alpine Orogeny all show relatively consistent east–west‐directed segmentation on the northern margin of Gondwana. This shows that they may have a unified dynamic genetic background. The zone of structural weakness formed by the collision of multiple terranes during the Pan‐African Orogeny may have controlled this segmentation. The inheritance between reformation of the pre‐Hercynian Palaeozoic basins and influence on the post‐Hercynian Mesozoic basins by Carboniferous–Early Permian Hercynian Orogeny, is the result of the tectonics repetitively focused in pre‐existing weaker domains, under the lithospheric mantle modification in the polyphase assembly and break‐up of the supercontinent.