Background Several neuroimaging studies demonstrated that visual deprivation led to significant cross-modal plasticity in the brain’s functional and anatomical architecture. Purpose To investigate the pattern of the interhemispheric functional connectivity in individuals with late blindness using the voxel-mirrored homotopic connectivity (VMHC) and seed-based functional connectivity (FC) methods. Material and Methods Forty-four individuals with late blindness (22 men, 22 women; mean age = 39.88 ± 12.84 years) and 55 sighted control individuals (35 men, 20 women; mean age = 43.13 ± 13.98 years)—closely matched for age, sex, and education—underwent resting-state magnetic resonance imaging scans. The VMHC and seed-based FC methods were applied to assess interhemispheric coordination in a voxel-wise manner. Results Compared with the sighted control groups, the late blindness groups showed decreased VMHC values in the bilateral cuneus/calcarine/lingual gyrus (CUN/CAL/LING) (BA 17/18/19) (voxel level: P < 0.001, Gaussian random field [GRF] correction, cluster level: P < 0.005). Meanwhile, for seed-based FC analysis, compared with the sighted control group, the late blindness group showed a decreased FC between the right lower VMHC regions and the bilateral CUN/LING/CAL/precuneus (PreCUN)/left middle occipital gyrus (MOG) (BA 18/19/30/31) and left precentral gyrus (PreCG) and postcentral gyrus (PostCG) (BA 2/3/4/6). The late blindness group showed a decreased FC between the left lower VMHC regions and the bilateral CUN/LING/CAL/PreCUN (BA 18/19/31) and left PreCG and PostCG (BA 2/3/4/6) relative to the sighted control group (voxel level: P < 0.001, GRF correction, cluster level: P < 0.005). Moreover, a negative correlation was observed between the duration of blindness and VMHC values in the bilateral CUN/CAL/LING (r = −0.393, P = 0.008) in individuals with late blindness. Conclusion Our results indicated that late blindness induced substantial impairment of interhemispheric coordination in the visual cortex. This might reflect impaired visual fusion, visual recognition function, and top-down modulations in individuals with late blindness.