In this study a new type of bifunctional phenolic compound based on a double-decker silsesquioxane (DDSQ-BP) was synthesized from phenyltrimethylsilane and then reacted (Mannich condensation) with allylamine and CH2O to form a bis-allyl benzoxazine DDSQ derivative (DDSQ-BZ). The structures of these DDSQ derivatives were confirmed using Fourier transform infrared and nuclear magnetic resonance spectroscopy and MALDI-TQF mass spectrometry. Highly thermally stable, transparent, and flexible polybenzoxaiine prepolymers were obtained after hydrosilylation of DDSQ-BZ with polydimethylsiloxane (PDMS) as the flexible segment; these materials were characterized using differential scanning calorimetry thermogravimetric analysis, Microtensile testing, and UV-vis spectroscopy. The char yield of DDSQ-BZ-PDMS was 73 wt%, significantly higher than that of a typical polybenzoxazine; in addition, DDSQ-BZ-PDMS displayed high flexibility and transparency after thermal curing.