This review provides a comprehensive and systematic overview of antimicrobial peptides (AMPs), including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, and future prospects. AMPs, which are small peptides found in nature, play a crucial role in the innate immune system of various organisms by inhibiting bacteria, fungi, parasites, and viruses. The emergence of antibiotic-resistant microorganisms and concerns about antibiotic use have driven the development of AMPs, which show promising applications in medicine, food, animal husbandry, agriculture, and aquaculture. AMPs are classified based on their sources (mammals, amphibians, insects, microorganisms), activity (antibacterial, antifungal, antiviral, antiparasitic, anticancer), and amino acid-rich species (proline-rich, tryptophan-rich, arginine-rich, histidine-rich, glycine-rich). The membrane-targeting mechanisms of AMPs include the toroidal pore model, barrel-stave model, and carpet-like model, while non-membrane targeting mechanisms involve inhibiting protein biosynthesis, nucleic acid biosynthesis, protease activity, and cell division. Design methods for AMPs include site-directed mutation, de novo design, template-based design, self-assembly, chemical modification (such as halogenation, cyclization, capping), and peptide conjugation. Synthetic mimics of AMPs (SMAMPs) and peptoids are also discussed as alternatives to natural AMPs. Motifs with specific functions, such as ATCUN, Rana box, LPS binding motif, γ-core motif, NGR motif, and "glycine zipper" motifs, are highlighted for their role in enhancing the activity and specificity of AMPs. The review also emphasizes the challenges and future directions in AMP research, particularly in addressing the issues of toxicity, stability, and cost-effectiveness. The COVID-19 pandemic has highlighted the urgent need for effective antiviral peptides, and the review discusses the potential of AMPs against coronaviruses, including the design of fusion inhibitors and the use of molecular docking to understand their mechanisms of action.This review provides a comprehensive and systematic overview of antimicrobial peptides (AMPs), including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, and future prospects. AMPs, which are small peptides found in nature, play a crucial role in the innate immune system of various organisms by inhibiting bacteria, fungi, parasites, and viruses. The emergence of antibiotic-resistant microorganisms and concerns about antibiotic use have driven the development of AMPs, which show promising applications in medicine, food, animal husbandry, agriculture, and aquaculture. AMPs are classified based on their sources (mammals, amphibians, insects, microorganisms), activity (antibacterial, antifungal, antiviral, antiparasitic, anticancer), and amino acid-rich species (proline-rich, tryptophan-rich, arginine-rich, histidine-rich, glycine-rich). The membrane-targeting mechanisms of AMPs include the toroidal pore model, barrel-stave model, and carpet-like model, while non-membrane targeting mechanisms involve inhibiting protein biosynthesis, nucleic acid biosynthesis, protease activity, and cell division. Design methods for AMPs include site-directed mutation, de novo design, template-based design, self-assembly, chemical modification (such as halogenation, cyclization, capping), and peptide conjugation. Synthetic mimics of AMPs (SMAMPs) and peptoids are also discussed as alternatives to natural AMPs. Motifs with specific functions, such as ATCUN, Rana box, LPS binding motif, γ-core motif, NGR motif, and "glycine zipper" motifs, are highlighted for their role in enhancing the activity and specificity of AMPs. The review also emphasizes the challenges and future directions in AMP research, particularly in addressing the issues of toxicity, stability, and cost-effectiveness. The COVID-19 pandemic has highlighted the urgent need for effective antiviral peptides, and the review discusses the potential of AMPs against coronaviruses, including the design of fusion inhibitors and the use of molecular docking to understand their mechanisms of action.