Purpose: To compare the effect of bilateral medial rectus injection of botulinum toxin A (BTX-A), bilateral medial rectus muscle recession surgery (BMR rc), or unilateral medial rectus muscle recession combined with lateral rectus muscle resection surgery (R&R), in the management of partially accommodative esotropia (PAET) in children.Design: Retrospective comparative clinical study.Methods: The study cohort included 98 patients diagnosed with PAET who had BTX-A injection or incisional surgery between December 2014 and January 2023. The main outcome measures included motor and sensory results as well as complications. Follow-up was at least 12 months for all patients.Results: There were 28 patients in the BTX-A group, 45 in the R&R group, and 25 in the BMR rc group. The motor success rates at distance and near fixation respectively were 50% (14/28) and 54% (15/28) in the BTX-A group, which were lower than that of the R&R group [78% (35/45), 84% (38/45)] and the BMR rc group [72% (18/25), 84% (21/25)] (P = 0.042 for near and P=0.006 for distance). For patients with onset age <2.5 years old, there was no statistical difference amongst the three surgical approaches (P=0.656). For patients with onset age ≥2.5 years, the motor success rate of the R&R group [81% (26/32)] and the BMR rc group [88% (14/16)] was higher than that in the BTX-A group [38% (5/13); P=0.004]. There was no statistical difference in sensory outcomes for patients regardless of onset age or treatment methods (P>0.05 for all). During follow-up, 4% (2/45) of patients in the R&R group and 20% (5/25) in the BMR rc group developed consecutive exotropia; no patient in the BTX-A group was overcorrected (P=0.017).Conclusions: Bilateral medial rectus muscle injection with BTX-A in patients with PAET is a safe, accessible, and low-cost alternative. Although motor success rates were higher, overall, in patients treated with incisional surgery, for patients with earlier age of onset (≤ 2.5 years old), BTX-A injection may be preferred to incisional surgery. In older children treated with unilateral recession-resection surgery, fewer developed consecutive exotropia.