Background <p>The neurovascular pathophysiology of migraine may extend to the retinal microvasculature. This study aimed to investigate structural and microvascular changes in migraine patients using optical coherence tomography angiography (OCT-A), focusing on the impact of migraine itself, independent of potential confounding factors.</p> Methods <p>In this prospective, observational study, 54 migraine patients and 55 age- and sex-matched healthy controls underwent comprehensive OCT-A imaging. Peripapillary retinal nerve fiber layer (RNFL) thickness, ganglion cell complex (GCC) thickness, and macular vessel density (VD) in the superficial (SCP), deep (DCP), and choriocapillaris (CC) plexuses were compared. Multivariable regression analysis was employed to control for age, sex, spherical equivalent, and blood pressure.</p> Results <p>Migraine patients exhibited significantly reduced vessel density in the inferior quadrants of both the SCP and DCP compared to controls (<i>p</i> &lt; 0.05). Notably, migraine status emerged as a significant independent predictor of reduced inferior DCP vessel density (β = -2.443, <i>p</i> = 0.044) after adjustment for confounders. Female sex was also an independent predictor of reduced VD. Strong negative correlations were observed between inferior DCP VD and clinical severity markers, including monthly attack frequency and MIDAS scores (<i>p</i> &lt; 0.01). A paradoxical increase in nasal CC VD was detected. No significant differences were found in RNFL, GCC, or central macular thickness.</p> Conclusions <p>This study identifies microvascular impairment in the inferior deep capillary plexus as a key, independent feature of migraine, strongly correlated with disease severity. OCT-A presents a promising tool for detecting objective biomarkers of migraine-related microvascular dysfunction.</p>