Due to storage stability drawbacks of polymer-modified bitumen (PMB), this study investigated the storage stability and physicochemical performance of Styrene-Butadiene-Styrene (SBS) asphalt binders (herein PMB) modified with Silicone surface-treated nanosilica (SNS). Dosages 0% (control), 1.5%, 3% and 5% SNS powder were added to PMB to prepare modified binders. Hot storage, Viscosity, Multiple Stress Creep Recovery (MSCR), Scanning Electron Microscopy (SEM), Fluorescence Microscopy (FM), Linear Amplitude Sweep (LAS), Fourier Transform Infrared (FTIR), and Proton Nuclear Magnetic Resonance (1H-NMR) tests were conducted using modified binders. The study found that adding nanosilica powder to PMB improved storage stability, increased viscosity and complex modulus, and reduced rutting of binders. However, this bitumen modification was not beneficial to fatigue cracking. The performance improvement was because of the interaction between the polymer and nanosilica, creating a new polymer-nanosilica network which lowered the dynamics around the SNS particles, thereby reducing phase separation. Further, the Silicone Si–O–Si backbone bond present in SNS modified asphalt binder reduced temperature sensitivity thereby preventing thermal degradation at high storage temperature. Nanosilica modified binders presented well-dispersed nanosilica particles in the asphalt matrix. The modification mechanism was predominantly physical. Overall, the study concluded that nanosilica improves storage stability, rutting, and morphology of PMB binders.