Abstract: Atomic force microscopy (AFM) is a modern microscopic and physical manipulation technology with an atomic resolution. The paper presents the AFM principle, technology development and the methodology advantages, and focuses on the application results of the characterization of starch structures at nanometer level, the topography, and the mechanism of film formation of maize zein, the dynamics of collagen type I, the relationship between lipid morphology and function, storage kinetics of fruits and the gene maps of Chinese alcohol, etc. The application of Nano Raman technology based on AFM in food science research will hopefully play an important role in the morphology, structure research and process control of food science.