High temperature instability is the biggest problem which limits the application of Styrene-Butadiene-Styrene (SBS) modified bitumen in flexible pavements. Addition of multi-layer graphene (MLG) nanomaterial improves the performance of SBS modified bitumen, but deteriorates its thermal stability. The binary additive comprising of MLG and multi-walled carbon nanotubes (MWCNT) can be a way to improve the thermal stability through their synergistic effects, however, mixing protocol needs to be optimized simultaneously. In this present study, MLG, MWCNT and their combination have been dispersed by two different organic solvent dissolution protocols, i.e., wet and dry to prepare the SBS-nano modified binders. Thermal stability analysis and rheological characterization (small & large amplitude oscillatory shear) have been used to optimize the method and to compare the effect of sole and binary additive. Advanced tools such as Raman spectroscopy and Field emission scanning electron microscopy have been used to understand the underlying science at micro-molecular level. The synergistic effects of combined additives are prominently visible only in dry organic dissolution method and with this method, the combination of MLG-MWCNT (0.1phr-1phr) significantly eliminates the thermal instability of SBS modified binder by upto 96 %. This SBS-nano modified bitumen may serve as futuristic binder for the black top pavements.