Long-term aging of bitumen causes formation of oxidation products that can be associated with polar and strongly interacting functional groups leading to a tremendous influence on bitumen properties. This can lead to an aggregation of the most polar molecules in the asphaltene fraction. Other types of aggregation have also been described in the literature, with larger and more aliphatic compounds through wax interactions. These aggregate phases can be studied using gel permeation chromatography (GPC) for the separation of heavy petroleum products based on their molecular weight. Three molecular weight fractions of native bitumen and its aged state by a long-term pressure aging vessel (PAV-72h) were obtained with low molecular weight (LMW), medium molecular weight (MMW), and high molecular weight (HMW) fractions. To characterize oxidative aging on each fraction at the molecular level, Fourier transform ion cyclotron resonance (FTICR) was used. Indeed, the ultrahigh resolution and mass accuracy of this analyzer allow to attribute molecular formulas to each signal of complex matrices unambiguously. An electrospray ionization (ESI) source was used to selectively ionize acid molecules, while atmospheric pressure photoionization source (APPI) was used to have a nonselective ionization of low polarity molecules from bitumen. With both ionization sources, the LMW fraction exhibited the most aromatic and heteroelement-enriched molecules. In terms of variation with aging, the LMW fraction showed the most pronounced variations. Molecular maps evidenced the occurrence of low DBE oxidation markers for Oz and OzSy families. Low variations were observed on distributions of MMW and HMW fractions. Concerning HMW, these unexpected results, obtained by ESI and APPI ionization sources, may be due to a protection of the molecules against oxidation within aggregates. In addition, APPI results underlined that the higher molecular weight distribution containing most of the aggregate molecules was mainly composed of large aliphatic molecules. Overall, this study demonstrated that oxidation products corresponded to small and aliphatic molecules majorly found in the LMW fraction and that aggregated molecules form HMW fraction were relatively protected from oxidation.