Previous studies of white matter (WM) had been limited to structural assessment. In this study, by utilizing resting-state fMRI, the BOLD signals in WM and its functional correlations with BOLD signals in grey matter (GM) were assessed between antipsychotic-naive schizophrenia patients and healthy comparisons. The functional correlation coefficient defined as GM-WM functional synchrony were found widespread altered in patients, especially in WM connecting hemispheres, fronto-temporal, cortico-subcortical regions, and in prefrontal, cingulate, visual, temporal cortex. Additionally, age and illness-duration related alternations in functional synchrony shared the same trend. These findings described schizophrenia as a progressive disorder which was characterized by dysconnectivity.