Abstract: Objective To study the confocal microscopy imaging of the cornea with fungal keratitis and its treatment outcome, explorer its role in the early diagnosis and appropriate treatment of fungal keratitis. Methods Between April, 2012 and April, 2013, 38 patients (38 eyes) suffered with fungal keratitis were examined in our hospital by corneal smears, fungal culture and corneal confocal microscopy before the treatment. All patients received natamycin eyedrop, amphotericin B eyedrop and fluconazole antifungal therapy. The confocal microscopy laser scanning was performed again to observe the density of hyphae and inflammatory cells in the corneal lesion at 7, 14 and 21 d after treatment and 7 d after drug withdrawal, and the treatment plan was adjusted based on the curative efficacy. All patients were followed up for one month to observe the relapse of fungal infection. Results Confocal microscopy detected the hypha in 34 patients with a positive rate of 89. 47%. The fungal hyphae was characterized by high refractive filaments which had branch. Fourteen cases (41. 18%) were in accordance with the characteristics of Fusarium spp. (branch angle 90°); 10 cases (29. 41%) in accordance with the characteristics of aspergillus (branch angles 45°); 2 cases (5. 88%) in accordance with the characteristics of yeast (slender granular). Thirty-one cases were cured with a rate of 81. 58%, 7 cases were improved; there was no worse and relapse cases. The average course was 19 days. The hyphae and inflammatory cells gradually reduced after treatment and disappeared after cures. Conclusion Confocal microscopy plays an important role in the early diagnosis of fungal keratitis, preliminary identification of strains and dynamic follow-up of treatment outcome. This is also a valuable objective tool in directing antifungal medication.