Based on a large quantity of data, this paper compiled lithofacies paleogeographic maps for the Early Triassic (247Ma), Middle Jurassic (170Ma), Late Cretaceous (85Ma), and Miocene (20Ma) in the East African region. These maps were produced through the analysis of seismic and geological profiles, drilling information, stratigraphic composite column charts, and evaluation data from new blocks. These maps are valuable guides for studying the prototype structures of hydrocarbon-bearing basins in the East African region, and finding oil–gas rich zone for future hydrocarbon exploration. This study indicates that the East African region has undergone multiple episodes of intraplate and interplate extension since the Permian period, resulting in the formation of two major types of basins: the East African passive continental margin basin group and the East African Rift System. The passive continental margin basin group experienced three evolutionary stages, including the Late Carboniferous-Triassic Karoo Rift, the Jurassic Madagascan Rift, and the passive continental margin from the Cretaceous to the present. This evolution resulted in a two-layer structural pattern, with terrestrial rift deposits overlying marine passive continental margin deposits. The East African Rift System can be divided into the Eastern and the Western branches, and has undergone multiple rifting events from the Oligocene to the Middle Miocene and from the Middle Miocene to the present. These events have shaped the current landscape of frequent volcanic activities and a distribution pattern of multiple lakes. Lithofacies paleogeographic analysis reveals that during the Early Triassic, the present-day East African region was part of the Gondwana supercontinent. Due to the Karoo Rift and plate separation, a trough was formed in the north of the Madagascan landmass, while the south to Mozambique was dominated by terrestrial deposits. During the Middle Jurassic, the separation of the African and Antarctic plates led to the extension of marine deposits into southern Mozambique, and the development of marine carbonate rocks along the Somalia-Tanzania-Madagascar margin. In the Late Cretaceous, Madagascar separated from East Africa, resulting in the initial formation of a passive continental margin structure. The East African margin was mainly composed of shallow to deep-marine deposits, and rift systems began to form in Kenya and Sudan. By the Miocene, the passive continental margin of East Africa had been established, with marine carbonate rocks developing only along the Kenya-Somalia margin and the western Madagascar. The rest of the region was dominated by shallow to deep-marine deposits, with local delta deposits developing along the edges of South Africa, Mozambique, and Kenya. The East African Rift System had also solidified, with the development of lacustrine deposits.