Objective To compare the motor and sensory outcomes and quality of life (QOL) of augmented medial rectus recession (aMRc) and botulinum toxin A (BTXA) therapy in acute acquired comitant esotropia (AACE) treatment and to investigate the predictors of recurrence. Methods We conducted a prospective, non-randomised clinical trial that enrolled 63 AACE patients with a disease course of 6 months to 2 years and deviation angles of 15 to 60 prism diopters. The patients were assigned to BTXA (n=31) and aMRc group (n=32). We compared and analysed the deviation angles, fusion amplitudes (FA) of convergence and divergence, stereopsis, and scores of QOL and diplopia between the two groups before treatment and at 2, 4, 6 and 12 months post-treatment. Results Both groups exhibited significant improvements in motor and sensory outcomes. The aMRc group showed more stable and satisfactory deviation than the BTXA group at 6 and 12 months post-treatment, with a significant increase in divergent FA. The aMRc group achieved a higher success rate (93.75%) than the BTXA group (64.52%) 1 year post-treatment. QOL improved significantly in both groups after treatment, except for reading function in the BTXA group. Compared with the BTXA group, the aMRc group showed greater improvements in self-perception, general function, and diplopia scores (p<0.05). Survival analysis revealed a significant difference between the two groups (p=0.0046). Treatment method and convergent FA at near before treatment were identified as recurrence predictors (p=0.023 and 0.025). Conclusions Augmented MRc treatment was superior to BTXA injection in AACE patients with courses >6 months during 1-year observation, particularly in maintaining alignment, eliminating diplopia and improving divergent FA and QOL. Trial registration number ChiCTR2300068735.