The intrinsic flammability of wood restricts its application in various fields. In this study, we constructed a phytic acid (PA)–silica hybrid system in wood by a vacuum-pressure impregnation process to improve its flame retardancy and smoke suppression. The system was derived from a simple mixture of PA and silica sol. Fourier transform infrared spectroscopy (FTIR) indicated an incorporation of the PA molecules into the silica network. Thermogravimetric (TG) analysis showed that the system greatly enhanced the char yield of wood from 1.5% to 32.1% (in air) and the thermal degradation rates were decreased. The limiting oxygen index (LOI) of the PA/silica-nanosol-treated wood was 47.3%. Cone calorimetry test (CCT) was conducted, which revealed large reductions in the heat release rate and smoke production rate. The appearance of the second heat release peak was delayed, indicating the enhanced thermal stability of the char residue. The mechanism underlying flame retardancy was analyzed by field-emission scanning electron microscope coupled with energy-dispersive spectroscopy (SEM-EDS), FTIR, and TG-FTIR. The improved flame retardancy and smoke-suppression property of the wood are mainly attributed to the formation of an intact and coherent char residue with crosslinked structures, which can protect against the transfer of heat and mass (flammable gases, smoke) during burning. Moreover, the hybrid system did not significantly alter the mechanical properties of wood, such as compressive strength and hardness. This approach can be extended to fabricate other phosphorus and silicon materials for enhancing the fire safety of wood.