In this work, vanillin based inherently flame retardant polyurethane/SiO2 composite foams were designed. Firstly, the vanillin based flame retarding diol (VDP) was synthesized. Then, the KH550 modified nano-SiO2 (KH550-g-SiO2) was prepared as the reinforcement. Subsequently, a series of flame-retardant polyurethane/SiO2 composite foams (PUF-0.5P-xSiO2) were synthesized by tailoring the hard-soft segments and KH550-g-SiO2 contents. The results showed that KH550-g-SiO2 significantly improve the thermal stability of the PUF-0.5P-xSiO2 foams. In addition, the compressive strength of PUF-0.5P-xSiO2 foams was enhanced from 0.18 MPa (PUF-0.5P) to 0.45 MPa (PUF-0.5P-2.0SiO2) under 20% strain. The flame retardant properties of PUF-0.5P-2.0SiO2 reached UL-94 V-0 grade. Meanwhile, the addition of KH550-g-SiO2 also decreased the thermal conductivity from 0.046 W/m·k to 0.037 W/m·k for PUF-0.5P-2.0SiO2. This work may provide an approach to obtain the biobased lightweight polyurethane foams for the application in packaging and building areas.