Objective To evaluate the safety and efficacy of multiple subconjunctival injections of conbercept for pterygium patients after surgery. Methods As a prospective randomised interventional trial, 96 eyes from 96 patients with a tendency to recur were collected and divided randomly into conbercept and 5-fluorouracil groups on the 5th day after pterygium. All patients received three subconjunctival injections of conbercept (0.2 ml) or 5-fluorouracil (0.2 ml) on the 5th day (baseline), and 2 and 4 weeks postoperatively. The pterygium morphology, colour intensity, recurrence, and complications were recorded and analysed pre-1st injection and 1 day, 1 week, 1 month, 3 months, and 6 months post-3rd injection. Moreover, no patient was drop-out. Results There were striking differences between the two groups on post-3rd injections 1 day, 1 week, 1 month, 3 months, and 6 months (p = 0.001, 0.002, 0.000, 0.000, and 0.002, respectively) with respect to colour intensity: the eyes in conbercept group were lighter than the 5-Fu group. On post-3rd injection 6 months, prominent disparities existed between the two groups with respect to pterygium morphology (p = 0.006) and recurrence (p = 0.002), occurred in the conbercept group prior to the 5-Fu group. Moreover, corneal abrasions were not noted in the conbercept group, which was significantly less than the 5-Fu group (17/48; p = 0.000). There was no conspicuous discrepancy between the two groups with respect to subconjunctival haemorrhage (p = 0.789) and persistent epithelial defects (p = 0.078). Conclusion Multiple subconjunctival conbercept injections as an adjunct therapy for pterygium surgery was shown to be safe, effective, and well-tolerated.