Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) with negative ion electrospray ionization (ESI-N) and positive ion atmospheric pressure photoionization (APPI-P), and compound-specific carbon isotope measurements together with conventional biomarker analyses were applied on 13 crude oil samples from Cretaceous reservoirs in the Shushan, Dahab/Mireir, and Abu Gharadig basins of the northern Western Desert of Egypt to identify their origin, maturity, alteration level, and petroleum relationships. Five oil families were identified, and the FT-ICR-MS data enabled a differentiation between crude oils with terrigenous, marine, and mixed organic matter input based on polar compounds. The dominance of acidic (ESI-N) and low-polarity (APPI-P) oxygen-containing compounds in the Shushan oils reflects land plant material input and oxic depositional conditions for their source rocks. The abundance of oxygen-containing compounds gradually decreases in the NE-Abu Gharadig and Dahab/Mireir oils (source rocks: mixed Type III/II organic matter (OM)) to reach minimum values in the marine-dominated Abu Gharadig oils. Based on compound-specific carbon isotopes and hydrocarbon biomarkers, the Shushan Basin hosts two different oil families from source rocks with Type III OM that likely reveal different thermal maturities and ages. The detected APPI-P aromatic hydrocarbons together with other molecular maturity ratios suggest a higher thermal maturity for the Shushan family A and Abu Gharadig oils than for oils of Shushan family B and from the Dahab/Mireir Basins, respectively.