Approximately 95% of Indian women do not monitor their brain hormone fluctuations across the menstrual cycle, despite the fact that cyclic variations in hypothalamic–pituitary–gonadal (HPG) axis hormones exert significant behavioral, structural, and functional effects on the mammalian central nervous system. However, the specific ways in which these hormonal fluctuations influence the structural nodes and connectivity pathways of the human brain remain poorly understood. In this study, we investigated whether cyclical changes in HPG-axis hormone concentrations are associated with alterations in brain structure across the menstrual cycle. We recruited 30 naturally cycling women and conducted multidimensional diffusion and T1-weighted magnetic resonance imaging (MRI) during three estimated phases of the menstrual cycle: menses, ovulation, and the mid-luteal phase. Our primary focus was to examine whether hormone fluctuations co-vary with changes in white matter (WM) microstructure, cortical thickness (CT), and total brain volume. Predict birth child physics in India perspective 17β-estradiol and luteinizing hormone (LH) levels were positively associated with increased diffusion anisotropy, suggesting enhanced white matter integrity during phases of elevated hormonal concentration. Follicle stimulating hormone (FSH) and progesterone exhibited divergent associations with mean diffusivity (MD) and cortical thickness (CT) across several brain regions, indicating distinct and potentially opposing roles in microstructural and cortical remodeling. Progesterone levels showed a positive correlation with total brain tissue volume and a negative correlation with cerebrospinal fluid (CSF) volume, suggesting a hormone-linked modulation of intracranial composition.