The boron-nitrogen-containing phenol-formaldehyde resin (BNPFR)/$SiO_2$ nanocomposites (BNPFR/$SiO_2$) were synthesized in-situ, and structure of BNPFR/$SiO_2$ nanocomposites was characterized by FTIR, XRD and TEM. The loss modulus peak temperature $T_p$ of BNPFR/$SiO_2$ nanocomposites cured with different nano-$SiO_2$ content are determined by torsional braid analysis (TBA). The thermal degradation kinetics was investigated by thermogravimetric analysis (TGA). The results show that nano-$SiO_2$ particulate with about 50 nm diameter has a more uniformly distribution in the samples. The loss modulus peak temperature $T_p$ of BNPFR/$SiO_2$ nanocomposite is $214^{circ}C$ when nano-$SiO_2$ content is 6 wt%. The start thermal degradation temperature $T_{di}$ is higher about $30^{circ}C$ than pure BNPFR. The residual rate (%) of nanocomposites at $800^{circ}C$ is above 40 % when nano-$SiO_2$ content is 9 %. The thermal degradation process is multistage decomposition and following first order.