Thermal oxidation has a significant effect on rheological and chemical properties of composite polymerized asphalt. In this study, polyethylenes (PE) and a multi-polymer (a type of anti-rutting agent) were incorporated into asphalt binders at four contents and the properties of polymer-asphalt composite systems were investigated through chemical functional group, molecular size, thermal behavior and rheological characteristics. Due to the formation of large conjugate structure by thermal oxidation, the carbonyl peak shifted to a lower wavenumber after a long-term aging procedure and the aging procedure increased the values of large molecular sizes. However, the degradation of PE played a dominant role during oxidation progress, which significantly decreased the LMS value of composite binders. Therefore the aging process changed the chemical compositions and element component distribution of binders and these changes were influenced by both binder source and polymer contents. In addition, with the increase of polymer modification, the penetration value and phase angle value at low frequency decreased; the endothermic peak area, softening point as well as complex shear modulus at low frequency increased. Therefore, the polymer degradation and polycyclic aromatic hydrocarbon formation should be considered during the aging process, which influenced the rheological performance of composite polymerized asphalts together. Furthermore, the correlation analysis showed that the carbonyl structure index I(C)dbnd(O) has significant correlations with the difference between glassy modulus and equilibrium modulus, and phase angle master curve plateau delta P, the LMS value has significant relationships with phase angle master curve factors delta L and delta P + delta L at a lowfrequency.