Background. Hemispheric asymmetry is one fundamental principle of neuronal organization. Interhemispheric connectivity and lateralization of intrinsic networks in the resting-state brain demonstrate the interhemispheric functional organization and can be affected by disease processes. This study aims to investigate the interhemispheric organization in children with dyskinetic cerebral palsy (DCP) based on resting-state functional MRI (fMRI). Methods. 24 children with DCP and 20 healthy children were included. Voxel-mirrored homotopic connectivity (VMHC) was calculated to detect the interhemispheric connectivity, and the lateralization of the resting-state networks was performed to examine the asymmetry of the intrinsic networks of brain. Results. Decreased interhemispheric connectivity was found at visual, motor, and motor-control related regions in children with DCP, while high cognitive related networks including the central executive network, the frontoparietal network, and the salience network represented decreased asymmetry in children with DCP. Abnormal VMHC in visual areas, as well as the altered lateralization in inferior parietal lobule and supplementary motor area, showed correlation with the gross motor function and activities of daily living in children with DCP. Conclusion. These findings indicate that the interhemispheric functional organization alteration exists in children with DCP, suggesting that abnormal interhemispheric interaction may be a pathophysiological mechanism of motor and cognitive dysfunction of CP.