<p>This study investigates the phase separation effects of PG 64–22 modified rubberized binders with two types of nanocomposite clays. Manual blending of crumb rubber modifier (CRM) and conditioning at 200&#xa0;°C for 1&#xa0;h were performed, followed by evaluating the binder properties under various curing and blending conditions. Performance characteristics and phase separational changes were assessed using Superpave and Multiple shear creep recovery (MSCR) test methods. The findings reveal that increasing mixing time and temperature results in reduced viscosity of the modified binder, whereas the incorporation of nanocomposite clays leads to increased viscosity. Additionally, the combination of extended mixing time, nanocomposite clays, and crumb rubber enhances the G*/Sin<InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(\delta\)</EquationSource> <EquationSource Format="MATHML"><math> <mi>δ</mi> </math></EquationSource> </InlineEquation> values, with the 3% kaolinite + 10% crumb rubber modified binder exhibiting the highest values. Moreover, the percentage recovery studies demonstrate an inverse relationship between blending duration, load cycles, and recovery percentages, with the 3% kaolinite + 10% crumb rubber modified binder displaying superior recovery. Furthermore, higher temperature and mixing time directly contribute to the reduction of phase separation between the asphaltene-rich and rubber-rich phases. Notably, the addition of nanocomposite clays as a secondary modifier has no impact on reducing phase separation. Finally, the 5% crumb rubber modified binder demonstrates a lower separation index (SI) percentage compared to all other combinations. These findings provide valuable insights for improving asphalt binder modification techniques and developing high-performance asphalt materials.</p>