Macroscale dysconnectivity in schizophrenia is associated with neuropathological abnormalities. The extent to which alterations in cortical myelination as revealed in vivo by magnetization transfer ratio (MTR) are related to macroscale dysconnectivity remains unknown. We acquired magnetization transfer imaging (MTI) data and diffusion weighted imaging (DWI) data from 78 schizophrenia patients and 93 healthy controls for MTR extraction and connectome reconstruction to examine the possible link between cortical myelination and macroscale dysconnectivity. Our findings showed significant cortical MTR disruptions in several prefrontal areas in schizophrenia patients, including bilateral rostral middle frontal areas, right pars orbitalis, and right frontal pole. Furthermore, cortical MTR alterations between patients and controls were significantly correlated with the level of regional disconnectivity. Together, our findings provide evidence that microstructural neuropathological abnormalities in schizophrenia are predominately present in prefrontal areas of the cortex and are associated with alterations in structural connectome architecture at the whole brain network level.