Based on the principles of microbial fermentation, cytoarchitectonics, and biomineralization, we have developed a novel synthetic method by which the multilayered nanostructure of yeast cell tissues can be copied by phosphates. Taking living yeast cells as catalytic templates and reactors, a series of hierarchical mesoporous Ca-, Zn-, Mg-, and Ti-phosphate-protein nanocomposites with complex surface shapes are synthesized under ambient conditions, and their scale-up syntheses are carried out. The results show that the structure and composition of the synthesized nanocomposites have good repetition and they can be produced in a large quantity. The mechanism of biomineralization for gene regulation in yeast cells was discussed. The present method has many advantages, including the mild reaction conditions, simple process, no pollution, and ease of industrial production.