To investigate neurovascular changes; including macular vascular density (VD), thickness of the ganglion cell layer (GCL) and optic nerve head (ONH) parameters in episodic migraine patients. 80 eyes of 40 episodic migraine patients were recruited. Thirty patients having a dominant side of migraine headache were statistically analyzed (5 male and 25 female; mean age 31.67 ± 9.54years) and compared to 25 eyes of 25 healthy volunteers (5 male and 20 female; mean age of 34.4 ± 12.11years, p = 0.361). The posterior segment was imaged with Topcon DRI optical coherence tomography (OCT) (Triton Swept source OCT Topcon, Japan), and OCT angiography (OCTA). Comparing the dominant side of migraine patients to controls we found a significant decrease of the VD in the central zone of the superficial and deep capillary plexus (SCP, p = 0.01; DCP, p = 0.004) and an enlarged foveal avascular zone (FAZ, p = 0.054). The GCL thickness was significantly reduced in the central ring (GCL + p = 0.042, GCL + + p = 0.029), as well as the retinal nerve fiber layer (RNFL) thickness in the temporal quadrant (p = 0.021) and border tissue of Elschnig diameter (BTE, p = 0.035). The duration of migraine showed an inverse correlation with SCP in the nasal quadrant (p = 0.016, r = - 0.445) and with all DCP regions [DCP superior (p = 0.004, r = - 0.519), DCP inferior (p = 0.004, r = - 0.519), DCP nasal (p = 0.006, r = - 0.496), DCP temporal (p = 0.005, r = - 0.508), DCP CSF (p < 0.001, r = - 0.634)]. The dominant side compared to the non-dominant side showed a significant deterioration of the VD in the inferior (p = 0.04) and temporal quadrants (p = 0.023); furthermore, a significant decrease in the GCL + + inner ring thickness (p = 0.046). Microvascular damage and consequent structural alterations of the retina and optic nerve head occur in the eyes of episodic migraine patient in association with the lateralization of the headache.