Many types of collagens from different sources have been used in food, pharmaceutics, biomedicine, tissue engineering, etc. Their physicochemical properties have been widely investigated to understand their behaviors and functions. However, the polymorphism and stability of collagen nanostructureshave not been systematically studied. In the current manuscript, polymorphism and stability of nanostructures of three types of collagens from bovine flexor tendon, rat tail, and tilapia skin are characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), atomic force microscopy (AFM), and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectrometry. SDS-PAGE results show loading volumes have no influence on the protein bands of three types of collagens except the intensity, whereas collagen concentrations have obvious effects. AFM results show all the three types of collagens have multiple nanostructures, which are concentration-dependent. AFM results also show collagen nanostructures change with incubation time at 37 °C. According to the ATR-FTIR results, the nanostructures changes are associated with the change of protein secondary structures. These results demonstrate three types of collagens have different nanostructures, stability, protein secondary structures, and SDS-PAGE behaviors. This work also indicates that the nanostructures and secondary structures of collagens can be controlled by adjusting concentration and incubation time for the three types of collagens, which provide simple ways to design and prepared desired nanostructures of collagen-based foods. It will be also beneficial to fundamental understanding of the collagen nanoscale structure formation in different collagen-based foods.