Foodborne pathogens pose a major threat to food safety, and they are able to develop stress resistance to many physical treatments (e.g., heating) and chemical agents (e.g., disinfectant) commonly used in food industries, making it easier to cause food poisoning. The development of stress resistance in foodborne pathogens is usually due to the coordinated function of multiple genes, sRNAs, proteins and metabolites, and these genetic elements are generally involved in multiple metabolic pathways. Recent advances in omics technologies have provided solid technical support for the exploration of genetic elements related to bacterial stress resistance and the characterization of their interaction networks, which will eventually contribute to the establishment of resistome databases for foodborne pathogens. In this context, this article provides a systematic overview on the application of genomics, transcriptomics, proteomics, and metabolomics technologies in research on stress resistance mechanisms in foodborne pathogens. Furthermore, future research perspectives are also presented to provide a theoretical basis to curb foodborne diseases caused by stress-resistant pathogens.