In early blindness, the primary visual area (PVA) loses the ability to process visual information, and shifts to working on the processing of somatosensory input, auditory input, and some higher-level cognitive functions. It has not yet been investigated whether such functional changes can lead to alterations of the functional connectivity between the PVA and other brain areas in resting state. The purpose of this study is to investigate the differences in the functional connectivity of the PVA between early blind and sighted subjects using resting functional MRI data. The altered functional connectivity was identified by comparing the correlation coefficients of the PVA with other brain areas between 16 early blind subjects (blindness onset within 1 year of age) and 32 gender- and age-matched healthy sighted volunteers. Compared with the sighted, the early blind subjects showed decreased functional connectivity between the left PVA and the bilateral supplementary motor area (SMA), pre- and postcentral gyri, superior parietal lobule, and the left superior and middle temporal gyri. Early blind subjects also showed decreased functional connectivity between the right PVA and the bilateral SMA, pre- and postcentral gyri. Our findings suggest that early deprivation of a single sensory modality induces alterations of functional connectivity between the deprived functional area and other associated brain areas.