Many systemic diseases like diabetes, hypertension, or microorganism infections and accident injuries may damage the eyes. Using specific light to enter eyes from the controlled environment, ophthalmologists use light-transmitted information obtained with special instruments like slit-lamp biomicroscopes for clinical diagnosis. In this review, the major structures of the eyes and their important functions will be introduced first. A brief picture of eye diseases is presented, includinginfectious, immune-related, congenital, degenerative, and traumatic entities. We finally focus on Raman spectroscopy, which is a novel qualitative and quantitative optical technique to probe biological systems with advantages including noninvasiveness, less sample volume needed, and utility even in aqueous environments. The purpose of this paper is to review the applications of this developing non-invasive technology in ophthalmological studies, especially in the diagnostic technology of microbial keratitis, which is a vision-threatening disease necessitating rapid and correct diagnosis. Additionally, some clinical approaches for diagnosing microbial keratitis will also be addressed to fill the gap between clinical methods and this novel technique. Raman-based analysis platform, a promising technique for microbial keratitis diagnosis, can bring a new era, especially for patients with microbial keratitis.