In the food field, a large number of phenomena and problems that are difficult to be macroscopically explained by traditional experimental methods occur during the process of research and development in upstream laboratories to production in downstream factories. Molecular simulation techniques are not only efficient and cost-effective, but also an important tool for connecting micro and macro scales, because molecular models can be used to study molecular behaviors at the atomic level, and thus predict and explain experimental results. This review summarized the commonly used software and databases for molecular simulation techniques, and introduced their applications in recent years in the fields of food safety, food processing and storage, and screening of food functional factors and their mechanisms.