The Quseir Formation consists mainly of dark gray mudstones with a high organic matter content and excellent hydrocarbon-generating potential. The main objectives of this study are to highlight the dominant structural elements in the Komombo Basin, Egypt, and evaluate the geochemical characteristics of the Quseir Formation. Depth maps and a 3D structural model indicate two normal fault trends NW–SE and ENE–WSW. The NW–SE trend is the dominant one that created the primary half-graben system. The depth to the top of the Quseir Formation gradually decreases from the eastern and central parts towards the corners of the basin. The thickness of the Quseir Formation ranges from about 300 to 1000 ft. The 3D facies model shows that the shale has a large probability distribution in the study area, compared with the sandstone and siltstone. The source rock potential varies between good in the western part to very good in the eastern part of the basin. The organic-rich interval is dominated by gas-prone kerogen type III based on TOC and Rock-Eval. The pyrolysis data vitrinite reflectance (%Ro) (0.5–0.74%) and Tmax values (406–454C°) suggest a maturity level that ranges from immature to early maturity stage for hydrocarbon generation.