Objective To observe and analyze the fungal species, risk factors and clinical characteristics in patients with fungal keratitis who underwent large-diameter penetrating keratoplasty (LDPK) in order to provide an objective basis for the diagnosis and treatment of fungal keratitis. Methods This was a retrospective case series study. Patients with fungal keratitis who were admitted to Qingdao Eye Hospital from January 2005 to December 2013 and underwent LDPK (graft diameter>9 mm), were selected for follow-up to monitor fungal species infections. One hundred and thirty-two cases (132 eyes) with fungal keratitis, including 82 males and 50 females, underwent LDPK. Of them, there were 76 farmers, 10 workers and 46 in other occupations. Data on the duration from the onset to the hospital visit, severity at diagnosis and clinical features of infection (including pseudopodia, satellite lesions, endothelial plaque, moss cover, hypopyon, ulcer area) were recorded. A descriptive and statistical analysis (χ² test) was performed on the differences in species and the relationship between the differences in clinical features. Results The infectious fungal species included 85 cases of Fusarium (64.4%), 10 cases of genus Aspergillus (7.6%), and 37 other cases. The mean duration from onset to LDPK surgery in all 132 cases was 23.7±11.2 days. The first three clinical features of Fusarium spp. were pseudopodia, hypopyon and satellite lesions; the first three clinical features of Aspergillus spp. were hypopyon, moss cover and pseudopodia. Compared with Aspergillus spp. (44.8±20.2 mm2), the ulcer area of Fusarium spp. (48.3±12.3 mm2) was larger, and occupied the entire cornea in 29 patients with Fusarium spp. Conclusion Fusarium spp. and Aspergillus spp. are common pathogenic fungi and may cause serious fungal infections that threaten eyeball preservation. The large amount of hypopyon is an important indicator of serious fungal infections. For patients poorly controlled with drugs, the early selection of corneal transplant surgery for disease control may provide a positive clinical treatment strategy.