Abstract: The development of next generation sequencing technology has driven a paradigm shift in the etiology of oral diseases from traditional pathogen detection to the study of microbiota ecological imbalance. The progress of next generation sequencing technology in diseases such as dental caries, periapical periodontitis and oral cancer was reviewed in the article, with the objective to analyze the development of this technology and its innovative applications in oral diseases, and to provide new ideas for the future analysis of the process from basic research on the oral microbiome to precise clinical diagnosis and treatment.