It is widely acknowledged that mild traumatic brain injury (MTBI) leads to either functionally or anatomically abnormal brain regions. Structural covariance networks (SCNs) that depict coordinated regional maturation patterns are commonly employed for investigating brain structural abnormalities. However, the dynamic nature of SCNs in individuals with MTBI who suffer from posttraumatic headache (PTH) and their potential as biomarkers have hitherto not been investigated.This study included 36 MTBI patients with PTH and 34 well-matched healthy controls (HCs). All participants underwent magnetic resonance imaging scans and were assessed with clinical measures during the acute and subacute phases. Structural covariance matrices of cortical thickness were generated for each group, and global as well as nodal network measures of SCNs were computed.MTBI patients with PTH demonstrated reduced headache impact and improved cognitive function from the acute to subacute phase. In terms of global network metrics, MTBI patients exhibited an abnormal normalized clustering coefficient compared to HCs during the acute phase, although no significant difference in the normalized clustering coefficient was observed between the groups during the subacute phase. Regarding nodal network metrics, MTBI patients displayed alterations in various brain regions from the acute to subacute phase, primarily concentrated in the prefrontal cortex (PFC).These findings indicate that the cortical thickness topography in the PFC determines the typical structural-covariance topology of the brain and may serve as an important biomarker for MTBI patients with PTH.