Spontaneous low-frequency oscillatory changes in oxygenated hemoglobin (oxy-Hb) and deoxygenated hemoglobin (deoxy-Hb) are observed using functional near-infrared spectroscopy (fNIRS). A previous study showed that the time-averaged phase difference between oxy-Hb and deoxy-Hb changes, referred to as hemoglobin phase of oxygenation and deoxygenation (hPod), is sensitive to the development of the cortex. We examined phase-locking index of hPod, referred to as hPodL, in addition to hPod, in neonates and 3- and 6-month-old infants using the 94-channel fNIRS data, which covered large lateral regions of the cortex. The results showed that (1) developmental changes in hPod exhibited spatial dependency; (2) hPodL increased between the neonate group and 3-month-old infant group over the posterior, but not anterior, regions of the cortex; and (3) the cortical regions of each age group were clustered in several domains with specific characteristics of hPod and hPodL. This study indicates that the neonatal cortex is composed of regions with specific characteristics of hPod and hPodL, and drastic changes occur between the neonatal period and 3 months of age. This study suggests that hPod and hPodL are sensitive to the cortical region-specific development of the circulatory, blood flow, metabolic, and neurovascular functions in young infants.