Nanoporous silica with unusual interior composite cells was synthesized with synthetic block copolypeptide Phe20-b-PBLG50 as template for the first time. Anilino-methyl triethoxy silane (AMTS) was used as an intermedium to interact with block copolypeptide Phe20-b-PBLG50 through π-π interaction between the phenyl groups of block copolypeptide and those of AMTS. Meanwhile, AMTS co-condenses together with tetraethoxylsilane (TEOS) after hydrolysis. The structure of composite vesicles due to the self-assembly of block copolypeptide in the organic solvent was immobilized and transcribed by the formation of silica. The formation of nanopores could be ascribed to the secondary structure of block copolypeptide and small molecular amine. Our results provide a new avenue to synthesize porous oxide materials with novel interior structures templated by the copolypeptide self-assembly under ambient conditions.