Biomineralization refers to a native biosynthesis process whereby the organisms fabricate hierarchical organic-inorganic composites for life maintenance, growth, and biological evolution. Motivated by these outstanding advantages, scientists endeavor to reproduce the manufacturing strategies and structural features of biomineralization by means of synergetic combination of inorganic materials and bioactive organisms. Thus, following the identified mechanisms of biomineralization, the biomimetic mineralization is becoming an emerging research field for designing and engineering organisms. In the present review, we summarize the recent achievements in understanding and applications of biomineralization-based organisms engineering. Aiming at design of application-oriented material-organism hybrids, we pay attention to the strategies that can endow organisms, such as viruses, bacteria, and cells, with addressable structures and excellent physiological properties, which can thereby facilitate the unnatural functions including environmental resistance, biological enhancement, tumor therapy, and cell-based delivery. By summarizing the recent research focus, we hope to provide an alternative understanding for the design and application of organism-material hybrid using biomineralization-inspired engineering.