Brain imaging studies have reported that the neural deficits of congenital amusia in non-tonal language speakers are mainly in the connectivity between the auditory cortex and the inferior frontal gyrus (IFG) in the right hemisphere. However, the relationship between the functional connectivity (FC) in these regions and the music perception ability of amusia in tonal language speakers remains unclear. In this study, we investigated the FC characteristics of amusia in Mandarin speakers in resting-state functional magnetic resonance imaging data by voxel-wise connectivity analyses with seeds in left and right Heschl's gyri (HG) and region of interest (ROI)-to-ROI connectivity analyses. Our findings indicate increased connectivity between right HG and bilateral posterior superior temporal gyrus, as determined by voxel-wise connectivity analyses in amusia. Conversely, reduced connectivity was observed between bilateral HG and bilateral IFG (orbital part) as assessed through ROI-to-ROI connectivity analyses in amusia when compared to controls. Moreover, the music perception scores of amusia in Mandarin speakers were associated with diminished connectivity between the left HG and the right IFG. This study furnishes direct evidence for the link between music perception deficits and the aberrant frontotemporal connectivity of congenital amusia in tonal language speakers in resting state.