To compare the prognosis and efficacy of acellular porcine corneal stroma (APCS) with different thicknesses for the treatment of fungal corneal ulcers by lamellar keratoplasty (LKP). A total of 52 patients who underwent LKP with APCS for the treatment of fungal corneal ulcers were included in this retrospective study. Patients were divided into 2 groups according to the different thicknesses of APCS (0.30 ± 0.05 mm, L2 group, n = 20; 0.40 ± 0.05 mm, L3 group, n = 32). Observation indicators included best corrected visual acuity, graft transparency, corneal neovascularization, ocular irritation symptoms, corneal epithelial healing time, graft survival, central corneal thickness at 1 year after surgery, and postoperative complications. Compared with the L3 group, the L2 group had better postoperative best corrected visual acuity and graft transparency (P < 0.001), less corneal neovascularization (P < 0.001), and lower incidence of complications (P < 0.05). There were significant differences in ocular irritation symptoms between the 2 groups (P < 0.05) at 3 and 6 months postoperatively, which might be related to the higher recurrence rate and graft rejection rate in the L3 group. The comparison of postoperative epithelial healing time also showed significant differences in 2 groups (P < 0.01). The 1-year survival rate was up to 63.5% in both groups, with no significant difference (P < 0.05). However, the risk of transplantation was less in the L2 group. Both APCS thicknesses could provide adequate central corneal thickness at 1 year after surgery (P > 0.05). APCS was safe and effective in the treatment of fungal corneal ulcers by LKP. Thinner grafts should be preferred for LKP for fungal corneal ulcers to reduce the risk of grafting.