This study evaluated cone density (CD) in the macular region and assess macular perfusion in children with varying degrees of myopia. This was a prospective, cross-sectional, observational study. Children underwent confocal scanning laser ophthalmoscopy (cSLO), optical coherence tomography (OCT), and OCT angiography (OCTA) imaging. A built-in software was used to measure mean CD (cells/mm2), retinal vessel density, choriocapillaris perfusion area, and choroidal thickness (CT). The study included 140 eyes from children categorized into four groups: emmetropia (31 eyes), low myopia (44 eyes), moderate myopia (31 eyes), and high myopia (34 eyes). The high myopia group exhibited significantly lower macular CD than the emmetropia group (P < 0.05). Additionally, the high myopia group showed thinner CT and higher choriocapillaris perfusion area in the macular region than the emmetropia group (all P < 0.01). Macular CD was significantly correlated with age, spherical equivalent, axial length, and CT (all P < 0.05). Generalized linear models revealed CT as the independent factor associated with macular CD (Wald χ2 = 9.265, P = 0.002). Children with high myopia demonstrate reduced CD in the macular region, accompanied by reduced CT. These findings may have important implications for future myopia prevention and management strategies.