The algae-derived bio-binder (ADBB) from hydrothermal liquefaction has been reported to be an effective and sustainable new alternative to petroleum-based curing agents for epoxy resin. However, there is still room for the epoxy/ADBB system to attain the comprehensive mechanical performance of conventional epoxy-based nanocomposites, typically reinforced with surface-functionalized nanofillers (e.g., glass nanoparticles (GNPs)) by petroleum-based silane coupling agents. Herein, we explored the use of ADBB as an innovative surface-modifying agent to functionalize GNPs and evaluated the potential of ADBB surface-functionalized GNPs (ADBB-GNPs) as a reinforcing agent in the epoxy/ADBB matrix nanocomposite by comparing them to pristine GNPs and (3-aminopropyl) triethoxysilane (APTES) (a popular silane coupling agent) surface-modified GNPs (APTES-GNPs). The surface functionalization of GNPs with ADBB was carried out and characterized by scanning electron microscopy (SEM), dynamic light scattering (DLS), and Fourier-transform infrared spectroscopy (FTIR). Material performance including tensile, flexural, and Izod impact properties and thermal properties of the resulting epoxy/ADBB nanocomposites were investigated by corresponding ASTM mechanical test standards and thermogravimetric analysis (TGA). Our results revealed that the ADBB is a sustainable and effective surface-modifying agent that can functionalize GNPs. The obtained ADBB-GNPs significantly improved the mechanical performance of the epoxy/ADBB system at ultra-low loading (0.5 wt.%) by up to 42% and the maximum decomposition rate temperature increased from 419 °C to 422 °C, both of which outperformed APTES-GNPs. This research sheds light on developing sustainable surface-modifying agents for nanofillers to create high-performance sustainable polymer composite materials.