Biomedical applications of porous calcium carbonate (CaCO3) microspheres have been mainly restricted by their aqueous instability and low remineralization rate. To overcome these obstacles, a novel symmetry-breaking assembled porous calcite microsphere (PCMS) was constructed in an ethanol/water mixed system using a two-step vapor-diffusion/aging crystallization strategy. In contrast to the conventional additive-induced crystallization method, the present strategy was performed under mild conditions and was free from any foreign additives, thus avoiding the potential contamination of the final product. Meanwhile, the prepared PCMSs were characterized by their highly uniform spherical morphology and large open pores, which are favorable for large protein delivery. An antimicrobial study of immunoglobulin Y (IgY)-loaded PCMSs revealed excellent antimicrobial activity against Streptococcus mutans. More importantly, they showed surprisingly rapid transformation to bone minerals in physiological medium. Evaluation of the in vitro efficacy of PCMSs in dentinal tubule occlusion demonstrated their powerful potential to serve as a catalyst in the repair of dental hard tissue. Therefore, the developed PCMSs show great promise as multifunctional biomaterials for dental treatment applications.