To determine the factors that affect ocular alignment and binocular sensory functions after strabismus surgery and compare surgical outcomes between manifest exotropia (XT) and esotropia (ET). In a retrospective study, 41 XT and 17 ET patients who had undergone strabismus surgery were recruited. Information on type and duration of strabismus, age at onset of deviation and surgery, pre- and postoperative strabismus deviation angles, and binocular sensory functions including stereoacuity and macular fusion capacity was recorded. In all patients, the ocular alignment and binocular sensory functions improved with time following surgery. Residue strabismus deviation angles (≦ 10 prism diopters) at postoperative 1month determined the final successful ocular alignment. In patients with final excellent binocular sensory functions, XT group restored macular fusion capacity and stereoacuity at postoperative 1month, but ET group regained macular fusion capacity at postoperative 1month and then restored stereoacuity at postoperative 3months. Though XT patients showed better pre- and postoperative stereoacuity than ET patients, patients with successful ocular alignment had an odd of 4.5 in XT group and 22.5 in ET group to achieve excellent and fair binocular sensory functions. Surgical correction of strabismus could improve ocular alignment and binocular sensory functions in patients with manifest strabismus, regardless of onset age, strabismus duration, or type. Postoperative 1-month status may help to predict the final motor and sensory outcomes. ET patients would benefit more final successful ocular alignment and excellent binocular sensory functions from early surgery and maintaining postoperative small deviation angle than XT patients.