Current threats of infectious diseases are severe, marked by prominent challenges such as emerging and re-emerging infections and antimicrobial resistance. Traditional prevention and control methods face limitations including lengthy development cycles, relatively narrow therapeutic targets and insufficient diagnostic sensitivity. Synthetic biology, an emerging interdisciplinary field, utilizes the “Design-Build-Test-Learn” (DBTL) cycle applied in numerous research studies within the biosecurity field. This review therefore focuses on the recent innovations and advances of synthetic biology techniques making the prevention and treatment of infections more efficient. For bacterial infections, these include engineered phage therapy, synthetic antimicrobial peptide design, and quorum sensing interference. For viral infections, the review covers intelligent diagnostic technologies, mRNA vaccines development, and CAR-T cell therapy. For invasive fungal diseases, the application of synthetic biology has enabled the discovery of novel drug targets and the development of antifungal nanomaterials. At the same time, however, the rapid advances in synthetic biology pose some other significant biological safety challenges. It is imperative to establish a tripartite combination that integrates institutional, technological, and ethical measures, thereby forging a development pathway that balances innovation efficacy with safety constraints. In conclusion, applying synthetic biology in infectious disease prevention uncontroversially offers novel routes to face severe biosecurity challenges.