Cyclosiloxanes possessing organic functional moieties are reactive organic–inorganic hybrids as effective building blocks for preparation of organic–inorganic nanocomposites. In this work, a tetra‐functional benzoxazine compound (cD4‐4Bz) with a cyclosiloxane core has been synthesized, cD4‐4Bz could be considered as a self‐crosslinkable benzoxazine compound and has been utilize in preparation of the corresponding polybenzoxazine‐cyclosiloxane thermosetting resins. The obtained crosslinked polybenzoxazines exhibit good film formability and attractive thermal properties including a thermal stability above 390°C, a glass transition temperature above 400°C, and a char yield of 64.5 wt% at 800°C, and low dielectric constant of 2.74 and a dissipation factor of 0.18 at 10 GHz. The hig char yield also indicates its high flame retardancy with a calculated limited oxygen index of 44. Moreover, cD4‐4Bz is a suitable agent for polymer modification through cocuring reactions with a tetrafunctional cyclosiloxane‐phenol compound, a main‐chain benzoxazine, and a bifunctional benzoxazine compound. One prepared sample has exhibited a high thermal stability above 435°C and a char yield of 72.9 wt%. The high flexibility and variety in the fabrication of high‐performance thermosetting resin have been demonstrated.