The formation of all biological structures, from single proteins, protein complex machines, cellular organelles, whole cells to intact organisms is driven by self-assembly with very complicated bio- regulatory mechanisms. In this review, characteristics of biological self-assembly and its physical, chemical and geometrical principles are summarized, and the bio-regulatory mechanisms of self- assembly are demonstrated by taking nascent peptide folding and chromosome condensation as examples. In recent years, principles of biological self-assembly have been applied to generate various functional nanostructures, such as DNA mechanical and electronic devices, DNA motors, protein nanowires, and biomolecular fluorescence complementation systems. Nevertheless, elucidating self-assembly of more complicated biological structures remains to be a great challenge. Learning the mechanisms allows us to better understand the essence of life and may give a big push to nanotechnology and bionics.