The Middle Jurassic Khatatba Formation, a source rock for hydrocarbons in Egypt's Matruh basin, was modeled using geological and geochemical data from the Apidose-1X well. The 1D basin modeling helps construct burial and thermal geo-histories and predict petroleum and expulsion timings. Using the straightforward cracking method of Sweeny and Burnham (1990), PetroMod-1D software created the burial history model of the Apidos-1X well. The end of the Cretaceous to Early Tertiary to Late Paleocene (60–58 Ma ago) was characterized by a major uplifting phase due to tectonic inversion. The constructed models indicate that the Khatatba Formation entered the onset of oil generation in the Early Cretaceous period (115–116 Ma ago), while the onset of gas generation took place in the Oligocene period (22–24 Ma ago). Cracking of oil to gas was observed in the Middle Jurassic source rock in the Apidose-1X well. The Matruh Basin includes all the elements of the petroleum system, with shale source rocks from the Middle Jurassic, sandstone reservoir rocks from the Early and Middle Jurassic, and seal rock from the Early Cretaceous. Oil generation, migration, and accumulation began in the Early Cretaceous, with hydrocarbons charging traps during rifting phases. The basin modeling results suggest that the Middle Jurassic source rock acts as an effective source rock, where a significant amount of petroleum is expected to be generated and expelled to nearby prospect reservoir rocks in the Matruh basin.