Foodborne pathogens will not only cause food spoilage and economic losses, but also have threats on human health. It is urgent to develop efficient and safe foodborne pathogen control strategies. In recent years, a great attention has been paid for research of probiotics in microbiology and food field. In addition to their functions of regulating and improving human health, probiotics and their metabolites have strong removal and inactivation effects on certain microorganisms, and have potential applications in the inhibition of foodborne pathogens. In order to elucidate types of probiotics and their metabolites, their underlying microbial inhibitory mechanisms, and their application status in food safety and quality control, it is crucial for the development of relevant control strategies of foodborne pathogen. This review focused on analyzing and summarizing the inhibitory mechanisms of existing probiotics and their metabolites on foodborne pathogens, and single- or multi-mechanisms including damaging cell structure, affecting replication of genetic substances, blocking energy metabolism pathways, interfering with quorum sensing systems, inhibiting biofilm formation and competition for key nutrients. At the same time, based on the current researches of the applications of probiotics and their metabolites in food safety and quality control, their application parameters and conditions, effects on shelf-life extension and qualities of fruits, vegetables and meat were discussed. The trends of their applications in active packaging and combining with other quality control strategies were also critically reviewed and highlighted. This review would provide meaningful references to the development of food safety and quality control based on probiotics and their metabolites.