Boron nitride nanoparticles (BNNPs) were surface functionalized and subsequently applied to surface of fiberglass prepregs to fabricate hybrid BNNPs/fiberglass/epoxy composite laminate. A systematic and comparative study on BNNPs functionalization routes and their effects on morphology, mechanical property and thermal conductivity of final BNNPs enhanced composite laminates was performed. The functionalized BNNPs were characterized by Fourier-transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM). The composite laminates with surface functionalized BNNPs demonstrated improvement in tensile and flexural strength and modulus as well as in thermal conductivity compared to the composite laminate with pristine BNNPs while physically functionalized BNNPs outperformed chemically functionalized BNNPs in all cases. SEM images indicated better compatibility and dispersion of BNNPs in epoxy matrix following either of functionalization route. BNNPs bear great radiation-shielding capability. This investigation revealed a novel and industrially feasible route to incorporate BNNPs in aerospace structural materials.