This study was performed to compare the thickness of the ganglion cell-inner plexiform layer (GCIPL) depending on the presence or absence of fixation preference in patients with intermittent exotropia (IXT) with refractive values close to emmetropia and with no amblyopia. The study recruited pediatric patients diagnosed with IXT with a spherical equivalent within ±1.25 diopter and no amblyopia. The patients were categorized into two groups: a monocular exotropia group with fixation preference and an alternating exotropia group without fixation preference. GCIPL thickness was measured using spectral domain optical coherence tomography, and the macula was divided into nine sectors according to the Early Treatment Diabetic Retinopathy Study (ETDRS). GCIPL thickness in each sector was compared between the monocular and alternating exotropia groups. In the monocular exotropia group, GCIPL thickness was significantly thinner in the dominant eye than in the nondominant eye in the S1 sector (91.2±7.4 μm vs. 93.3±5.2 μm, p=0.019). However, in the alternating exotropia group, there were no significant differences between the eyes across all ETDRS sectors. When comparing the interocular differences in GCIPL thickness between the two groups, the monocular exotropia group (absolute value of the dominant eye minus the nondominant eye) exhibited significantly greater differences in several ETDRS sectors than the alternating exotropia group (absolute value of the right eye minus the left eye). The significant interocular difference in GCIPL thickness in the monocular exotropia group suggests that fixation preference may influence the anatomical structure of the macula in patients with IXT.