The inherent properties of hard asphalt binder give it both mechanical and economic benefits, rendering it a naturally advantageous material for preventing permanent deformation at higher temperatures. However, its poor resistance to thermal and fatigue cracking limits its application in the paving industry. This study aimed to improve the low-temperature and fatigue performance of hard asphalt binders by using the newly developed vegetable oil-based sub-epoxidized rapeseed oil (SERO). Two SEROs with epoxidation degree of 49.1% and 98.1% were synthesized through an oxidation reaction, respectively. Subsequently, the microstructural characteristics of SEROs were examined by Fourier transform infrared spectroscopy (FTIR) and Hydrogen nuclear magnetic resonance tests. The anti-oxidative aging properties of SERO modified hard asphalt binders were investigated through the utilization of mass loss and aging index. Additionally, the comprehensive rheological properties of SERO modified hard asphalt binders were explored via dynamic shear rheometer and bending beam rheometer tests. Furthermore, the modification mechanism of SERO on hard asphalt binders was confirmed through the quantitative analysis using the FTIR test. The findings suggested the improvement in anti-volatilization and anti-oxidative aging performance of bio-modified hard asphalt binders, which was positively related to the epoxidation degree of SERO. A notable softening effect of SERO on the hard asphalt binders was observed, which enhanced their resistance to thermal and fatigue cracking at lower and intermediate temperatures. The epoxy groups within SERO engaged in ring-opening reactions, forming a new oxygen bridge bond by combining with the unsaturated double bond presented in the asphalt. Consequently, this process resulted in the formation of cross-linked structures within bio-modified hard asphalt binders, thereby enhancing the elasticity. Notably, this phenomenon was most conspicuous in the SERO-H modified 50# binder. Finally, the environmental and economic assessment of SERO modified hard asphalt binders were conducted by the techno-economic method and the emission factors technique. The data revealed that the production of one ton of SERO modified hard asphalt binders could reduce the production costs by about 30%, energy consumption and CO2 emissions by around 20% in contrast to styrene–butadiene–styrene block copolymer modified asphalt binders. Hence, the substantial economic and environmental advantages make SERO an attractive bio-renewable additive for sustainable pavements.