Objective To compare the clinical effects of limbal stem cell transplantation and amniotic membrane transplantation on pterygium. Methods A total of 130 patients （142 eyes） with pterygium admitted from January 2018 to June 2020 were selected as study subjects and autologous were divided into two groups according to treatment methods. The 65 patients （70 eyes） treated with pterygium resection and limbal stem cell transplantation were included in group A, and another 65 patients （72 eyes） treated with pterygium resection and amniotic membrane transplantation were included in group B. Corneal wound healing time, corneal astigmatism, tear film stability, and reactive hyperemia index were recorded, and recurrence after surgery were also observed. Results The corneal wound healing time in the group A[（4.58±1.04） d] was shorter than that in the group B [（6.85±1.22） d] （P<0.05）. After 1 week of surgery, the tear film stability was significantly better （P<0.05）, and the reactive hyperemia index was significantly lower （P<0.05） in the group A than in the group B. After 1 month of surgery, the corneal astigmatisms of the two groups were both improved than before, and there was no significant difference between the two groups （P>0.05）. After 3 months of surgery, the recurrence rate in the group A （3.08%） was significantly lower than that in the group B （13.85%） （P<0.05）. Conclusion Both autologous limbal stem cell transplantation and amniotic membrane transplantation for the treatment of pterygium can improve patients’ corneal astigmatism. However, autologous limbal stem cells are derived from autologous ocular surface tissues and produce fewer rejection reactions, so they are more helpful for wound healing and recurrence reduction.