Graphene nanoplatelets (Gnps) were covalently functionalized by 3-aminopropyltriethoxysilane (KH550) and noncovalently functionalized by Triton X-100, respectively. The morphology and structure of KH550 modified graphene (K-Gnp) and Triton X-100 modified graphene (T-Gnp) were characterized by Fourier transform infrared spectroscopy, scanning electron micrograph, and Raman spectrometer. The influences of K-Gnp and T-Gnp on thermal conductivity, fracture toughness, and thermal stability of the boron phenolic resin (BPR) were investigated. Both covalently functionalized K-Gnp and noncovalently functionalized T-Gnp not only improve the dispersion of Gnp in the polymer matrix but also increase interfacial bonding strength between the BPR matrix and Gnp, thus leading to the enhanced mechanical property and thermal stability of nanocomposites. Besides this, mechanical property and thermal stability of the BPR containing K-Gnp are superior to those of BPR containing T-Gnp.