Research on neonatal brain development reveals that the neonatal period is crucial for brain maturation, yet the connections between structural changes and functional reorganization remain unclear. A study involving 399 neonates, including 348 term-born and 51 preterm-born infants, examined the dynamic structure-function coupling (SFC) in brain networks using multi-modal MRI data. The findings indicate that dynamic SFC varies significantly across the neocortex and increases with postmenstrual age, especially in the default mode network (DMN). The study highlights that the dynamic SFC in the posterior DMN mediates the link between cortical microstructure, measured by the T1w/T2w ratio, and network flexibility. Preterm infants showed a notably reduced dynamic SFC compared to term-born infants, with an altered developmental trajectory in the DMN attributed to premature exposure outside the womb. These results suggest that dynamic SFC, particularly in the DMN, may serve as a biomarker for neonatal brain maturation, providing insights into the early development of internal cognition and its susceptibility to challenges faced in early life.