The mechanism of flavor formation in fermented aquatic foods is complex. The microbial interactions during the fermentation process leads to the formation of a variety of flavor components, so it is difficult to analyze the flavor components of fermented aquatic foods from a single perspective. In recent years, multiple-level omics which researches the regulation of gene expression, protein transcription and translation, protein-protein interactions, and the qualitative and quantitative analysis of metabolites has been applied to determine the characteristic flavor components and the mechanism of flavor formation in fermented aquatic foods. More broadly, omics can be used to build the metabolic network of flavor compounds and explore the relationship between flavor-related microorganisms and enzymes. This article reviews the main metabolic pathways involved in flavor formation in fermented aquatic products and recent progress in the application of multi-omics technology for analyzing flavor formation in aquatic products during fermentation and highlights its important role in the study of the flavor of fermented aquatic products.