This book presents a complete description and review of novel properties and mechanisms of form of hydrogen bonded structure and proton transfer as well as their extensive applications in physical and biological systems. In these investigations, the properties of hydrogen bond and hydrogen bonded system, the theory and properties of proton transfer in hydrogen-bonded systems and its experimental evidences in ice crystal, the behaviours of hydrogen-bonded structure and proton transfer in water and gramicidin A as well as influences of externally applied field on them, the features of hydrogen-bonded structure and soliton theory of proton transfer in DNA and its relationship with biological functions, the biological function and molecular structure of rhodopsin and bathorhodopsin as well as their characters of proton transfer and proton pump are described concretely and in detail. These contents are presented and stated in five chapters, respectively.