Messenger RNA (mRNA) vaccines, as a revolutionary biological product, have shown great potential in the prevention and treatment of infectious diseases. Compared with novel DNA vaccines, mRNA vaccines avoid the risk of genome integration, and their cell-free production significantly accelerates development and improves production efficiency compared with protein vaccines, which have been widely used. mRNA vaccines are able to encode multiple antigens, adapt to a variety of pathogen variants, and effectively stimulate strong immune responses with the dual functions of encoding antigens and adjuvants. However, further optimization of mRNA stability, immunogenicity and safety, as well as improvement of the efficiency of the delivery system, especially the application of lipid nanoparticles (LNPs), remain key challenges for the development of this technology. Globally, the successful application of mRNA vaccines in diseases such as neocollagenic infections has driven a new direction in vaccine development, heralding their potential role in the prevention and treatment of a wider range of diseases. Recent advances in sequence optimization strategies and delivery systems for mRNA vaccines as well as their applications in infectious diseases are reviewed, aiming to provide a comprehensive reference for future research and applications.