This paper reports a case of fungal keratitis (FK) in a 62-year-old male patient who was infected with Colletotrichum fructicola (C. fructicola) after plant-related trauma. Pathogen from patient was not clearly identified by two examination during hospitalization in other hospitals two months ago. Patient was confirmed with C. fructicola keratitis through confocal microscopy, corneal scraping, culture, and gene sequencing. The treatment of voriconazole combined with amphotericin B was adopted to enhance antifungal therapy, and anterior chamber irrigation, drug (voriconazole) injection in anterior chamber and corneal stromal as well as corneal lesion removal were performed. The patient’s symptoms were then improved. For patients with plant-related trauma keratitis, it is important to be alert to the possibility of rare fungal infection.