The report describes a rare case of microsporidian stromal keratitis in a 69-year-old farmer with a 5-month history of eye redness, pain, photophobia, and epiphora, complicated by corneal perforation. In vivo confocal microscopy (IVCM) revealed hyperreflective double-walled spore capsules and vesicular clusters as the earliest diagnostic features of microsporidia infection. Confirmation came from next-generation metagenomic sequencing (mNGS) and histopathology, which identified Microsporidia species. The patient underwent therapeutic penetrating keratoplasty followed by targeted antimicrosporidian therapy, which resulted in preservation of the globe and improved vision. IVCM serves as a non-invasive and rapid tool for early diagnosis, especially for atypical manifestations. This method detects microsporidian structures in real time and complements molecular techniques such as mNGS. MSK is a rare corneal disorder with insidious progression, requiring high clinical vigilance.