Lactic acid bacteria and the fermentation environment interact to form an intertwined system. Lactic acid bacteria are constantly evolving to adapt to different fermentation environments, causing changes in their physiological processes. To achieve a targeted improvement of their adaptability to various environments, a detail analysis of their evolutionary physiological processes is required. While several studies have been carried out in the past by using single-omics techniques to investigate their response to environmental stress, most researchers are now using a multi-omics approach to explore more detail in the biological regulatory networks and molecular mechanisms of lactic acid bacteria in response to environmental stress, thereby overcoming the limitations of single- omics analysis. In this review, we describe the various single-omics approaches that have been used to study environmental stress in lactic acid bacteria, present the advantages of various multi-omics combined analysis approaches, and discuss the potential and practicality of applying emerging single-cell transcriptomics and single-cell metabolomics techniques to the molecular mechanism study of microbes response to environmental stress. Multi-omics approaches enable the accurate identification of complex microbial physiological processes in different environments, allow people to comprehensively reveal the molecular mechanisms of microbes response to stress from different perspectives. Single-cell omics techniques, analyze the targeted regulation of microbial functions in a multi-dimensional space, provides a new perspective on understanding microbes responses environment stress.