Background Fungal keratitis is a common ocular surface disease and the treatment is dissatisfactory because of short of high efficiency,low toxicity and broad-spectrum medication.Penetrating keratoplasty is an effective therapy,but its clinical applications is limited due to lack of corneal donor.To seek a low-cost and effective management is of an important significance.Objective This clinical trial was to compare the clinical effectiveness between corneal ulcer debridement combined with amniotic membrane cover+drugs therapy and corneal ulcer debridement of combined drugs therapy for fungal keratitis.Methods A prospective cases-controlled study was designed.A total 210 eyes of 210 patients with fungal keratitis were included from January 2001 to January 2013 in Affiliated Hospital of Qingdao University.The patients were randomly divided into observation group (109 eyes) and control group (101 eyes).The combination therapy of corneal ulcer debridement with amniotic membrane cover and drugs was administered in the observational group,and only lesion debridement and drugs therapy was performed on the control group.The curative effect,postoperative visual acuity and therapeutic course were compared between the two groups.Results The effective rates for fungal keratitis were 100.00％,90.41％,77.78％ in the mild,moderate and severe patients,respectively,and those of the control group were 52.38％,80.00％,25.00％ respectively,showing significant differences between them (U =2.211,2.214,2.356,all at P＜0.05).The total effective rate was significantly higher in the observational group than that in the control group (91.09％ versus 75.23％),with a significant difference between them (U=3.040,P=0.002).Postoperative visual acuity was better in the observational group than that in the control group (0.44 ± 0.04 versus 0.22 ± 0.03),with a significant difference between them (t =2.225,P ＜ 0.05).The mean therapeutic course was (22.4 ± 1.8) days in the observational group,which is shorter than (33.2±2.4) days in the control group,with a significant difference between them (t =2.097,P＜0.05).Conclusions Combination therapy of lesion debridement with amniotic membrane coverage and drugs can shorten treating duration and improve vision,and it is superior to only lesion debridement and drugs therapy.