This paper introduces a novel toughened polymer mortar designed for runway repair, featuring outstanding impact resistance, high strength, and cost-effectiveness. To augment the toughness of unsaturated polyester (UP) polymer mortar, nano-SiO2 and polyurethane (PU) were incorporated. Firstly, the optimal dosages of nano-SiO2 and PU were determined through tensile test and impact test. Then, the modification mechanism of nano-SiO2/PU on UP resin was explored by microscopic image technology. In addition, the compression, flexural, fluidity, flexural bond strength and construction time tests were carried out to determine the optimal formula of nano-SiO2/PU modified UP resin mortar. Finally, the durability, impact resistance, impermeability resistance, skid resistance, and interlayer bond strength of modified UP resin mortar were studied and compared with those of pure UP resin mortar and epoxy (EP) resin mortar. Results show that the optimum proportion by mass for nano-SiO2/polyurethane modified UP resin is, UP resin: PU: dibutyltin dilaurate: nano-SiO2: initiator: accelerator: diluent: plasticizer = 1: 0.1: 0.002: 0.01: 0.01: 0.01:0.15:0.01. Furthermore, the mass proportion of modified UP resin to aggregate is 1: 1.2. In nano-SiO2/PU modification of UP resin, the -NCO groups of PU have been involved in chemical interaction with the -OH group of UP, while nano-SiO2 and UP resin are blended physically only. Compared with pure UP resin mortar, the nano-SiO2/PU modified UP resin mortar exhibited a 44% reduction in shrinkage rate, approximately 20% less corrosion loss, a 32% decrease in freeze-thaw loss, a 37% improvement in impact resistance, and increased shear bonding strength, flexural bonding strength, and tensile bonding strength by 44%, 33%, and 47%, respectively. Although the modified UP resin mortar demonstrated slightly lower performance in terms of dry shrinkage, corrosion resistance, skid resistance, and tensile bond strength compared to EP resin mortar, its freeze-thaw durability, impact resistance, flexural bond strength, and shear bond strength surpassed those of EP resin mortar. All three materials exhibited excellent impermeability. Leveraging the advantages of PU and nano-SiO2, the modified UP resin presents a promising repair material for airport pavement with enhanced toughness, high stability, and reduced cost.