Bacterial keratitis is a common infectious ophthalmopathy characterized by acute onset, rapid progression and high blindness rate. The key to its diagnosis and treatment lies in rapid and accurate identification of pathogenic microorganisms and formulation of individualized treatment strategies. At present, the changes of pathogen spectrum and drug resistance of bacterial keratitis have brought new challenges to clinical diagnosis and treatment, and traditional diagnostic methods are difficult to meet the clinical needs. Next generation sequencing (NGS) technology provides a new choice for etiological diagnosis of bacterial keratitis due to its advantages of high throughput, wide coverage, high sensitivity and rapid response. This review introduces the core principles of NGS technology and its current status in medical applications, focuses on the application progress of this technology in accurate diagnosis, drug resistance detection and epidemiological monitoring of bacterial keratitis, and discusses the future development direction and clinical transformation prospects, so as to provide reference for its application in accurate diagnosis and treatment of infectious keratitis.