Fermentation is a food preservation method with a long history. Fermentation not only give a unique flavor and taste of sea food, but also improve the nutrition value dut to enzymes and microbial metabolic activities. Fermented aquatic products can not only give aquatic products unique flavor and taste, but also increase the nutritional value of aquatic products. With the development of high-throughput sequencing technology and the creation and improvement of genomic databases, metagenomic composition is an important tool for studying the microbial community structure of fermented aquatic foods, the interaction between microorganisms, and functional gene mining. Lactobacillus, Staphylococcus and Saccharomyses have a close relationship with the quality of fermentation aquatic products, and is commonly used as starter in the production of fermented aquatic products. This paper reviews the research method of microbial community in recent years and microbial community structure and success in the fermentation process, to explore the effects of microorganisms on the quality formation of traditional fermented aquatic products. The research direction of the relationship has been prospected in order to provide effective theoretical basis for quality consensus and industrial production in the fermentation water product industry.