Objective To evaluate the safety and efficacy of bio-artificial cornea used in deep lamellar keratoplasty (DLK) in the treatment of infectious keratitis. Methods In this prospective noncomparative case series study, 20 cases with infectious keratitis were treated by DLK using bio-artificial corneas from December 2013 to November 2014 in Eye Hospital of Wenzhou Medical University. The best corrected visual acuity (BCVA), transparency of bio-artificial corneas, slit lamp biomicroscope examinations before and after surgery were analyzed. The follow-up period was 6 months. The blindness relief rate and infection control rate were evaluated, and the postoperative improvements in BCVA were analyzed by repeated measures ANOVA, and the transparency of bio-artificial corneas were compared using Wilcoxon test. Results The preoperative BCVA was less than 0.05 in every case with a mean of 2.08±0.35 (LogMAR). The mean BCVA improved to 0.44±0.26 (LogMAR) 6 months after surgery (F=94.97, P<0.01). The bio-artificial cornea edema lessened quickly in the first postoperative week and became transparent since 1 month after surgery (χ²=66.34, P<0.01). One case developed a recurrence of fungal infection. Another case developed stromal rejection. The blindness relief rate was 19/19 and the infection control rate was 19/20 in the patients who fulfilled 6-month follow-up. Conclusion The 6-month outcomes showed that the bio-artificial cornea is a safe and effective alternative used in DLK to treat infectious keratitis. The bio-artificial cornea has advantages in keeping cornea transparency after DLK and the visual acuity improved significantly.