Abstract: Novel physical processing technologies, such as ultra-high pressure, pulsed electric field, cold plasma, ultrasonic waves, and magnetic field, are profoundly changing the modern food processing landscape due to their advantages, including high efficiency, energy conservation, and operational safety. However, existing studies primarily focus on the macro level, such as process parameter optimization, nutritional quality regulation, and functional characteristic development, and have not systematically clarified the operating mechanisms at the micro level. In particular, there is still limited knowledge regarding hydrogen bond breaking and rearrangement behaviors. To deeply analyze the influence of physical processing on the intrinsic structure and function of food components, this work first reviews the association between hydrogen bond networks and the structure and functionality of major food components (water, polysaccharides, proteins, and multi-component systems) at the molecular level. It investigates the key roles of hydrogen bonds in physical and chemical processes such as water freezing, starch gelatinization–retrogradation, and protein denaturation and gelation. Based on this, and using the spatiotemporal dynamics of hydrogen bond network rearrangement as a clue, this study preliminarily reveals the microscopic mechanisms of phase transformation and texture evolution during the processing. Second, this study systematically reviews the mechanisms by which various new physical processing techniques regulate the structure and function of food components by disrupting hydrogen bond networks: the enhancement of hydration structures and the rearrangement of water molecules under ultra-high pressure; the promotion of the oscillation of polar molecules through electric field pulsation induced by the pulsed electric field; intermolecular cross-linking and group activation initiated by active species in cold plasma; bond breakage and free radical generation induced by ultrasonic cavitation effect in localized high-temperature and high-pressure areas; as well as the interference and orientation effects of the magnetic field on the dipole moments of polar molecules. To understand the complex process of hydrogen bonds at the microscopic scale, this paper also reviews the characteristics and applications of current hydrogen bond analysis techniques and explores the qualitative and quantitative capabilities of methods such as Raman and nuclear magnetic resonance spectroscopy in analyzing hydrogen bond types, concentrations, and state changes. Additionally, this study examines the application of microscopic imaging techniques, such as atomic force microscopy, cryo-electron microscopy and fluorescence lifetime imaging, in the visualization and characterization of microstructure, as well as the advantages of computer simulation (molecular dynamics) in the prediction of hydrogen bond formation, breaking and regeneration mechanisms, and the potential of multimodal combination strategies in revealing the complex process of "breaking - rearrangement". These advanced detection and analysis methods not only provide visual or quantitative insights into the microscopic changes occurring in food components during physical processing but also build a bridge between subsequent functional evaluation and mechanistic research. Finally, to promote the application of advanced detection technologies and improve the comprehensive analysis of hydrogen bond evolution paths, this paper proposes several key directions for future research, including strengthening theoretical research, developing intelligent monitoring systems, and adopting multi-dimensional analytical methods. Therefore, this study reviews the influence of new physical processing methods on the structure and function of food components from the perspective of hydrogen bond network rearrangement, and also provides valuable insights and references for the in-depth development of scientific research in the field of food processing. Overall, this article aims to promote the development of high-quality physical processing technologies in the food industry.