Silica aerogels (SA) have exceptional thermal insulation capabilities, however, their superhydrophobic nature hinders the formation of a uniform composite when combined with cement slurry. To address this issue, an aqueous solution was employed to disperse SA particles using sodium dodecyl sulfate (SDS). Subsequently, the dispersed micelles were coated with polydopamine (PDA) through in situ polymerization. This approach effectively enhanced the dispersion of SA in cement slurry and improved its connection force with the cement hydration products, thereby mitigating the adverse effects of aggregated SA on the mechanical properties of the cement composite. The successful PDA coating led to the formation of smaller aggregated micelles, resulting in a 30% improvement in compressive strength of cement composites containing modified SA compared to those using unmodified SA, while maintaining the desired thermal conductivity properties. With a strategic increase in the quantity of modified SA, a remarkable thermal conductivity of 0.1351 W/m·K was achieved without significantly compromising the compressive strength, which reached about 13.94 MPa. This enhanced compressive strength surpassed that of conventional thermal insulation materials like expanded polystyrene (EPS) and foam concrete. Consequently, this novel technique has the potential to markedly enhance the thermal insulation of cement composites without excessively impacting their compressive strength, thus contributing to the development of green insulation and energy-saving building materials.