The mechanical properties and durability of cement-based materials reinforced by nano-SiO2 (NS) particles are strongly dependent on the dispersion characteristics of the latter. This study presents an innovative eco-friendly method, which improves the distribution of NS particles through their surface modification using polycarboxylate ether-based (PCE) superplasticizer containing silane coupling agent under microwave irradiation. The above method ensures the formation of a core-shell-shell structure, wherein the PCE shell exhibits enhanced electrostatic and steric hindrance repulsion properties. Moreover, after the surface modification, an improved compatibility between NS and PCE and a higher dispersion stability of NS in the saturated calcium hydroxide solution are attained, which is proved by the respective grafting ratios and encapsulation parameters of the surface-modified NS particles. The proposed method application guarantees an enhanced fluidity of a fresh cement paste, which makes it lucrative for the production of critical components from nano-reinforced cement-based materials.