The work aims to find spoilage bacteria and pathogenic microorganisms through the dynamic analysis of microbial community structure during the processing and storage of aquatic products, so as to further improve the quality of aquatic products and extend their shelf life. Based on the introduction of the main characteristics and development process of high-throughput sequencing technology, the application of high-throughput sequencing technology in the processing and storage of aquatic products, such as the production of fermentation products, identification of adulterated adulterants, detection of food borne pathogens and spoilage bacteria were emphatically elaborated. The existing problems were analyzed and solved, and the development prospect of high-throughput sequencing technology was prospected. With the continuous development of biotechnology in the future, sequencing technology with low cost, short time and high accuracy will gradually replace the traditional detection methods and be better applied in aquatic product quality evaluation and microbial diversity analysis.