Fumed silica nanoparticles (FSNPs) have shown significant potential in polymer modification due to their economic viability. This study aims to explore the impact of FSNPs on the performance of high viscosity modified asphalt (HVMA). For a comprehensive view, we also introduced Nano-SiO2 and Nano-TiO2, common nano-modifiers, for comparison with the results achieved by FSNPs. The morphology of these nano-modifiers was observed with Field Emission Scanning Electron Microscopy (FESEM). The changes in rheological, chemical, and thermal properties of HVMA before and after modification were evaluated using techniques such as Dynamic Shear Rheometer (DSR), Fluorescence Microscope, Fourier Transform Infrared Spectroscopy (FTIR), and Thermogravimetric Analysis-Differential Scanning Calorimetry (TGA-DSC). The FESEM results revealed that FSNPs form a branchlike network while Nano-SiO2 and Nano-TiO2 lack specific structures or clear interconnections. Further rheological testing reveals that, when compared to Nano-SiO2 and Nano-TiO2, FSNPs improve the high-temperature performance of HVMA by 2–3 times and bolster its fatigue resistance by 1.2–3 times, while reducing temperature sensitivity. These enhancements are attributed to the synergistic strengthening between the FSNP's branchlike network and the SBS polymer network structure, underlining the significance of FSNPs' shape and connectivity in HVMA rheological property improvement.