AIM: To evaluate the efficacy and safety of decellularized conjunctival stroma (DCS) as a novel biomaterial by comparing its grafting outcomes with amniotic membrane (AM) when used for conjunctival reconstruction after primary pterygium excision. METHODS: This randomized, parallel-controlled study with allocation concealment enrolled 40 patients with primary pterygium. Participants were randomly assigned to two groups using the sealed envelope method: the DCS group (n=20) and the AM group (n=18), receiving DCS and AM grafts respectively. Slit-lamp photography of the operative eyes was performed preoperatively and at 1, 3, 5, 7, 10, 30, 90, and 180d postoperatively. Best-corrected visual acuity (BCVA) and symptom scores were recorded simultaneously. In vivo confocal microscopy was conducted at 3 and 6mo postoperatively. RESULTS: All participants exhibited improved postoperative symptoms. The mean age was 60±9y (male/female ratio: 6/14) in the DCS group and 56±12y (male/female ratio: 7/11) in the AM group. The average epithelial healing time was 9.89±3.54d in the DCS group and 8.17±1.34d in the AM group (P=0.084). One recurrence case was observed in each group. Postoperative graft hemorrhage was significantly more severe in the DCS group than in the AM group only at 30d postoperatively (P=0.011). In vivo confocal microscopy revealed conjunctival epithelial cell growth in both groups at 90d postoperatively, while clear corneo-conjunctival cell boundaries were observed until 180d postoperatively. CONCLUSION: DCS used in primary pterygium surgery has a safety profile comparable to AM. It promotes rapid postoperative conjunctival healing, achieves a relatively low pterygium recurrence rate, and yields outcomes similar to AM. DCS provides a novel biomaterial option for conjunctival reconstruction after pterygium excision and the treatment of other conjunctival injuries.