In this work, a highly flexible bio-silica reinforced poly (benzoxazine-co-epoxy) hybrid composites have been developed using renewable cardanol based benzoxazine (C-aee), commercially available bisphenol-F epoxy (EP) and functionalized bio-silica (BS). Sustainable C-aee was synthesized with cardanol (C), aminoethoxyethanol (aee), and paraformaldehyde through Mannich condensation reaction. The structure of C-aee monomer was characterized with FT-IR and (HNMR)-H-1 techniques. Bio-silica (BS) was synthesized from rice husk and functionalized with 3-mercaptopropyl trimethoxysilane (3-MPTMS). Later, the hybrid PC-aee-co-EP/BS composites was prepared with various weight percentages (0, 1, 3, and 5%) of BS reinforced into PC-aee-co-EP. The curing performance of C-aee, C-aee + EP and thermal properties of PC-aee-co-EP/BS composites was characterized using DSC and TGA. Data acquired from thermal studies confirmed that the bio-silica reinforced hybrid composite show improved thermal properties and flame-resistance properties with good flexibility. Hence, the developed PC-aee-co-EP/BS composites are potential material for various applications including marine coating, aerospace, and microelectronics.