Background: This study investigates the relationship between retinal vascularization and macular function in patients with cone dystrophies (CDs). Methods: Twenty CD patients (40 eyes) and 20 healthy controls (20 eyes) were enrolled in this prospective case-control study. Patients underwent full ophthalmological examination, microperimetry, full-field, pattern and multifocal electroretinogram (ERG, PERG, mfERG) and optical coherence tomography angiography (OCTA). Main outcome measures were as follows: foveal and parafoveal inner and outer retinal thickness; microperimetry sensitivity in the central 4° and 8°, ERG b wave amplitudes and peak times, PERG P50 and N95 amplitudes and latencies, and mfERG N1 to P1 amplitudes; and superficial capillary plexus (SCP), deep capillary plexus (DCP) and choriocapillary (CC) plexus vessel densities, divided into foveal and parafoveal region. Results: Retinal thickness, SCP and DCP densities were significantly related to PERG. A significant relationship was found between foveal and parafoveal retinal thicknesses and foveal SCP density (p < 0.001 and p = 0.018, respectively) and between parafoveal retinal thickness and parafoveal SCP density (p = 0.002). Foveal and parafoveal retinal thicknesses were significantly related to parafoveal DCP density (p = 0.007 and p < 0.001). Foveal and parafoveal retinal thicknesses, foveal SCP and parafoveal DPC densities were significantly reduced in CD patients compared to controls (p < 0.001; p = 0.010 and p = 0.008, respectively). PERG and mfERG amplitudes were significantly reduced in CD patients compared to controls (p < 0.01). Conclusions: CD eyes showed reduced retinal thickness significantly related to reduced vessel density, possibly caused by a decreased metabolic demand. In addition, vessel density significantly correlated with loss of function.