(1) Background: Amblyopia is an ocular condition leading to structural and functional changes. The relationship between these changes is complex and remains poorly understood. (2) Methods: Participants included 31 children aged 5 to 9 years with strabismic (n = 9), anisometropic (n = 16) and mixed (n = 6) unilateral amblyopia, and 14 age-matched non-amblyopic children. The 95% and 63% Bivariate Contour Ellipse Area (BCEA), axial length, Foveal Avascular Zone (FAZ) area, center macular thickness and volume were assessed. The relationship between these parameters was explored. (3) Results: Statistically significant differences were found among the four groups in best corrected distance visual acuity (BCVA) (p < 0.001), BCEA 95% (p = 0.002) and BCEA 63% (p = 0.002), but not in the FAZ area, central macular thickness, central macular volume and axial length. Eyes with amblyopia had poorer BCVA and larger fixation instability than controls. Inter-ocular differences were more significant in patients with strabismic amblyopia, particularly in BCVA (p = 0.003), central macular thickness (p < 0.001) and central macular volume (p = 0.002). In amblyopic eyes, BCEA 95% and 63% were correlated with BCVA, but not with the FAZ area. (4) Conclusion: Amblyopia is associated with a reduction in fixation stability and BCVA, although there is a general lack of correlation with structural changes, suggesting a complex interaction between anatomy and function in amblyopia.