Purpose Our objective was to investigate whether there were differences in the short-term changes of retinal and choroidal microvasculature between amblyopic and non-amblyopic eyes after patch occlusion treatment in patients with monocular amblyopia. Additionally, we aimed to determine if these changes were associated with improvements in clinical parameters. Methods We conducted a retrospective, longitudinal paired-eye case-control study by analyzing the medical records of patients under the age of 12 who had monocular amblyopia and underwent patch occlusion treatment for a duration of 2 to 12 months. Using optical coherence tomography angiography images, we compared the foveal avascular zone width, retinal blood vessel density (VD), choroidal thickness (CT), and choroidal vascularity index (CVI) in amblyopic and non-amblyopic eyes before and after patch occlusion treatment. We analyzed the correlations between the aforementioned parameters and changes in best-corrected visual acuity (BCVA) and stereopsis. Results Overall, 114 eyes from 57 patients were enrolled. At baseline, parafoveal superficial plexus VD, foveal and parafoveal deep capillary plexus VD (DCPD) were lower by 0.994 ± 3.312% (p = .026), 2.403 ± 8.273% (p = .033), and 2.469 ± 4.095% (p < .001), respectively; CT was thicker by 30.6 ± 90.7 μm (p = .014); and CVI was higher by 1.920 ± 3.432% (p < 001) in the amblyopic eyes than in the non-amblyopic eyes. Following short-term patch occlusion treatment, foveal and parafoveal DCPD increased by 1.264 ± 3.829% (p = .017) and 1.028 ± 3.662% (p = .036), respectively, CT thinned by 15.5 ± 51.5 μm (p = .019), and CVI decreased by 1.296 ± 3.997% (p = .018) in the amblyopic eyes. Following patch occlusion treatment, as the foveal DCPD decreased and CVI increased, the BCVA improved (p = .017 and .035, respectively). Conclusion Following patch occlusion treatment, increased foveal DCPD and decreased CVI were associated with improved BCVA.