Amblyopia is a developmental visual disorder that causes substantial visual deficits. Studies using resting-state functional magnetic resonance imaging have disclosed abnormal brain functional connectivity (FC) both across long-range cortical sites and within the visual cortex in amblyopes, which is considered to be related to impaired visual functions. However, little work has examined whether restoring the vision of amblyopes accompanies with an improvement of FC. Here in adult amblyopes and healthy participants, we compared their brain FC before and after an altered-reality adaptation training. Before the training, the voxel-wise FCs of amblyopia patients were substantially weaker than those of healthy control participants both within and across the early visual areas. After the training, visual acuities improved in amblyopes but not in the control participants. The effect kept strengthening in the subsequent month without further adaptation. Importantly, we observed enhanced voxel-wise FC both within and across the early visual areas of amblyopes. Moreover, the enhancement continued for at least 1 month. These results suggest that the effective treatment can improve both the amblyopes' vision and functional connections in the visual cortex.