Background: The aim of this study was to observe the effectiveness of botulinum toxin type A (BTA) in the treatment of intermittent exotropia (IXT) in children compared with strabismus surgery. Methods: One hundred forty-four children with a clear diagnosis of IXT and an indication for surgery were eligible for inclusion. Subjects were divided into two groups based on parental decision: the BTA injection group (injection group) or the conventional surgery group (surgery group). All cases were followed up for 6 months. The primary outcome was a comparison of the success rate (deviation between - 10 and + 10 PD) between the two groups at 6 months after the initial treatment. Secondary outcomes included change in deviation, visual function, and post-surgical complications. Results: Seventy-two patients were enrolled in each group. At 6-month follow-up, there was no significant difference in the success rate between the injection and surgery groups (52.8% vs 66.7%, P = 0.13; postoperative deviation - 12.22 +/- 10.80 PD vs - 9.17 +/- 10.30 PD, P = 0.09). The binocular Visual function, except for near stereoacuity, improved after treatment in both groups, while the fusion recovery rate was higher in the surgical group (68.1% vs 95.8%, P < 0.001). Transient complications in the injection group included diplopia, ptosis, and subconjunctival hemorrhage, whereas subconjunctival hemorrhage, conjunctival edema, foreign body sensation, pain, and diplopia were seen in the surgical group. The complications of BTA were relatively mild. Conclusions: BTA is as effective as surgery in the treatment of IXT in children, but the recovery of the fusion is lower than surgery.