Rett syndrome (RTT) is characterized by trajectory changes in cognition and motor functions. To understand the disease-specific pathologic changes of each tract bundle in white matter in stable stage of RTT, we applied tract-specific analysis of the whole brain to investigate the alteration of 76 major tracts by diffusion spectrum image. In conclusion, the altered microstructural integrity in RTT were covered in whole brain, however, in systematically view, most of them were located in associative and commissure tract bundles. Surprisingly, the GFA value of anterior commissure in RTT was higher than controls, which might explain the well-preserved visual perception clinically.