Herein, we report significantly enhanced mechanical properties and thermal conductivity of polyimide (PI) by incorporating a small amount (0.01 wt %) of individualized boron-doped high-quality graphene as a filler. The boron-doped expandable graphite (B-EG) was synthesized by mixing boric acid ( H3BO4) with expandable graphite (EG) and thermally treating the mixture at 2450 °C for 30 min using a graphite furnace in an argon atmosphere. The boron-doped graphene (B-g) was prepared by the solution-phase exfoliation of B-EG with an ultrasonication process, which is a method to obtain individualized graphene as well as few-layer graphene. The PI nanocomposites were prepared using the obtained graphene. The PI nanocomposites synthesized with high-quality B-graphene (B-g) showed enhanced mechanical properties and thermal conductivity compared to those of pure PI due to the doping effects and strong interfacial interactions between graphene and the PI matrix.