<p>This study systematically summarizes natural antibacterial agents and their derivatives derived from plants, animals, and microorganisms, deeply analyzes the binding and damage mechanisms of these antibacterial agents to bacterial cell membranes, and comprehensively reviews their applications in food, medical, textile, and other fields. Plant-derived antibacterial agents exert antibacterial activity through two key pathways. One is direct binding to pathogen cell proteins, which inhibits enzymatic activity; the other is disruption of bacterial cell membranes, leading to leakage of intracellular substances. The active components in essential oils can change the fluidity and permeability of cell membranes, and polyphenols can inhibit the formation of bacterial biofilms. Chitosan can affect the potential balance and material transport of cell membranes through interactions with bacterial cells. The innovation of this study lies in the detailed elaboration of three models of cell membrane disruption by biopeptides-the “barrel-stave model”, the “carpet model”, and the “toroidal pore model”-at the molecular and cellular levels. The key characteristics of the interactions between antibacterial peptides and cell membranes in each model were clarified and verified with experimental data. At the same time, the mechanism of phenolic substances disrupting the membrane potential balance was deeply explored, and the details of intermolecular interactions were elucidated, filling some gaps in the research on molecular mechanisms in this field. In addition, this study systematically summarizes and compares the applications of natural antibacterial agents from different sources for the first time, providing a reference for their rational application in different industries. This study provides a comprehensive theoretical framework and practical guidance for subsequent research. It is expected to promote the wide application of natural antibacterial agents in multiple fields, provide new strategies and approaches for solving the problem of antibiotic resistance, and contribute to the sustainable development of the food, medical, and textile industries. This review is the first to compare the differences in the effects of antibacterial agents from different sources on different types of bacteria, and verifies membrane damage models using experimental data. It fills the research gap in bridging “structure-activity relationship and application”.</p>