The Egyptian lower Eocene carbonate rocks (Thebes Formation) are part of an extensive carbonate platform formed during an eustatic regression along the Tethyan Ocean's southern margin. These rocks are essential in developing Egypt's petroleum system because they can operate as vertical seals in specific basins or as source-reservoir rocks. However, few in-depth studies have been conducted to explore the diagenetic history, pore system, petrophysical characteristics, and sequence stratigraphic framework of these rocks and its relationship to the global sequences. Multiple datasets (foraminiferal assemblages, petrographic, and petrophysical data) from the lower Eocene strata exposed in Wadi El-Dakhl and El-Sheikh Fadl sections on the western side of the Gulf of Suez were integrated. The biostratigraphic examination of the planktic foraminifera shows that three Eocene biozones (E5–E7) were identified in the studied successions. The reservoir quality index and the flow zone indicator show that reservoir quality ranges from poor to fair and good. The primary reservoir porosity was resulted from diagenetic processes, including dissolution, fracturing, and meteoric diagenesis, which enhanced reservoir quality. The inferred benthic foraminifera and petrographic studies indicate a shallowing upward trend and deposition in fluctuating settings ranging from upper slope to middle shelf. This progressive reduction in the relative sea level corresponds to a gradual eustatic decline and demonstrates the enhanced control of tectonic activity and eustasy. Consequently, the Thebes Formation was deposited due to Tethyan sea-level changes, and its pore system was influenced by tectonics associated with the Syrian Arc system and Gulf of Suez rifting.