Background Cone dystrophy is a hereditary retinopathy characterized by profound vision loss resulting from the degeneration of photoreceptors. Optical coherence tomography angiography (OCTA) is a technique that non-invasively visualizes the microvasculatures of the retina and choroid in detail. This study evaluates macular vessel density in Iraqi patients diagnosed with cone dystrophy using OCTA and makes a comparison with those of healthy controls. Methods The cross-sectional study was conducted at the Gazi Al-Harrir for Surgical Specialty Hospital from December 2021 to May 2024. Twenty-eight patients diagnosed with cone dystrophy and 28 healthy controls were evaluated based on measurement of best corrected visual acuity and thorough funduscopic examination. OCTA assessment of macular vessel density was performed in the central, superior, inferior, nasal, and temporal regions. All the statistical analyses were done with the software Jamovi (https://www.jamovi.org/): descriptive statistics, Shapiro-Wilk tests for normality, and independent samples t-tests. Results The mean central retinal thickness (CRT) was significantly lower in the cone dystrophy group (180.8 µm) compared to the control group (238.8 µm). Regarding macular vessel density, no significant differences were observed between the cone dystrophy and control groups in the central (13.4 µm vs. 17.7 µm, p = 0.234), superior (51.1 µm vs. 48.7 µm, p = 0.400), nasal (44.2 µm vs. 43.4 µm, p = 0.544), and temporal (45.1 µm vs. 45.5 µm, p = 0.202) regions. However, in the inferior region, a significant reduction in macular vessel density was observed in the control group compared to cone dystrophy patients (48.7 µm vs. 46.7 µm, p = 0.008). The Shapiro-Wilk test confirmed normal distribution for most parameters, and significant differences were identified using t-tests. Conclusion This study confirms that the macular vessel density is significantly reduced in Iraqi patients with cone dystrophy. OCTA proves to be a valuable tool for detecting these vascular changes that could act as biomarkers for the severity and progression of this disease. Longitudinal studies in the future are necessary to know more about these vascular alterations and their implications for treatment strategies.