Next generation sequencing (NGS) is a new sequencing method invented at the beginning of the 21^st century on the basis of first-generation sequencing technology. With its high throughput, high accuracy and abundant genetic data, NGS has been gradually applied to the dairy industry and has played an important role in ensuring the quality and safety of dairy products. On the one hand, this paper introduces the application of whole genome sequencing (WGS) technology to identify contaminated microorganisms, pathogen traceability, strain polymorphism, antibiotic resistance and virulence factor carrying status analysis. On the other hand, this paper focuses on the application of metagenomic sequencing technology in research on the application of microbial diversity, including microbial diversity investigation in the processing environment of dairy products, environmental microorganism monitoring of dairy factories, shelf-life assessment of dairy products, microbial risk monitoring of raw materials, and authenticity assessment of dairy products. Finally, this paper comprehensively analyzes and discusses the challenges and future prospects for the application of NGS technology in the field of dairy products.