In this study, a low-cost thermoset such as unsaturated polyester resin (UPR) was used for the preparation of lightweight and thermal insulation polymer composite using rice husk-derived silica aerogel (SA) as filler. For the first time, hydrophilic and hydrophobic silica aerogel (SA) of similar physical properties were added to the UPR to study the effects of SA surface polarity on the mechanical tensile and thermal properties of the composites. The composites with 40% and 60% of SA filler by volume were prepared via direct mixing and cured at room temperature using methyl ethyl ketone peroxide. The UPR composites were characterized and compared using density measurement, hot-disc thermal conductivity analyzer, universal testing machine, Fourier transform infrared spectroscopy, scanning electron microscopy and thermogravimetric analysis. The results of this study indicate that the filler–matrix interaction appears to be dependent on the type of SA (hydrophobic or hydrophilic), due to noticeable differences in the data values. UPR composites containing hydrophilic SA exhibit lower density and thermal conductivity due to a higher volume of preserved SA pores. Both hydrophobic and hydrophilic SA could increase the tensile stiffness, but composite with hydrophilic SA exhibit higher fracture strain, indicating higher toughness. On the other hand, composites with hydrophobic SA produced stronger hydrogen bonding interaction which increases resin viscosity and led to rougher surface morphology. However, the addition of SA, regardless of surface polarity and volume concentration had little or no effect on thermal stability except that the composite with hydrophobic SA gives a slightly higher char yield.