Conduct disorder (CD) is a common psychiatric disorder defined by a repetitive and persistent pattern of aggressive and antisocial behaviors. Although numerous task-based and resting-state functional magnetic resonance imaging (rsfMRI) studies have emphasized the disrupted functional connectivity in CD, the CD-related alterations in functional interactions between the bilateral cerebral hemispheres are rarely investigated directly. In this study, a voxel-mirrored homotopic connectivity (VMHC) method based on rsfMRI was employed for the first time to examine the abnormalities of interhemispheric functional connectivity in patients with CD. The VMHC was compared between eighteen pure CD patients and eighteen typically developing (TD) healthy controls. In CD patients, reduced homotopic connectivity was observed relative to TDs in the middle occipital gyrus (MOG), pre- and postcentral gyrus, rolandic operculum and paracentral lobe (PCL) which were the components of visual and motor networks. Furthermore, the VMHC of the MOG and PCL was found to be negatively correlated with clinical scores in the CD group. Moreover, the regions with altered VMHC exhibited a relative good and robust ability to discriminate CD patients from TDs. This study provided a novel angle to identify the important role of interhemispheric coordination in the pathophysiology underlying CD and further indicated that the aberrant homotopic connectivity could be a potential clinical neural marker for CD diagnosis.