Novel protein-based nanocomposites were well prepared by in vivo synthesis and co-precipitation of soy protein isolate (SPI) with calcium carbonate (CaCO3) in an aqueous solution. The resultant CaCO3 in the nanocomposites was identified as calcite- and aragonite-type, respectively. The morphology and structure of the CaCO3/SPI composites were investigated by means of wide-angle X-ray diffraction, Fourier transform infrared spectra, scanning electron microscopy, and high-resolution transmission electron microscopy. The results revealed that the polymorph and the size of CaCO3 in the nanocomposites were dependent on its content, pH, and the conformation of soy protein. At the content of more than 5%, CaCO3 was changed into calcite crystal with the preference of growing along (104) plane. However, at lower content of less than 5%, CaCO3 preferred to form aragonite in the composite as a result of the modulation by soy protein. The aragonite nanocrystals were arrayed in the direction of (111) plane and self-assembled along beta-sheet planes of soy protein polypeptides. The mechanical properties, thermal stability, and water resistance of the CaCO3/SPI nanocomposites were significantly improved as a result of the nanosized effects. Interestingly, the aragonite/SPI nanocomposite exhibited higher tensile strength (about 50 MPa) than that of calcite/SPI, owing to a good compatibility and strong interaction between aragonite and soy protein polypeptides. This work provided a simple pathway to develop the soy protein-based bio-hybrid materials with high mechanical strength and valuable information on their structure-properties relationship.