Objective In resting-state functional magnetic resonance imaging (fMRI) study, spontaneous activity patterns changed in anisometropic amblyopia could be reflected by the abnormalities of functional connectivity in visual network. Methods Twenty one adult anisometropic amblyopia and 21 normal controls participated in this study. Preprocessing with denoising and alignment, the fMRI data was analyzed to get functional connectivity value in three visual networks: the visuospatial network (VSN) , the high-level visual network (HVN) and the primary visual network (PVN) . Two sample t test was carried out to analysis functional connectivity value within the whole brain for the inter groups. Results We found a significant loss of correlation within VSN and HVN but not in PVN, and further the correlation between the VSN-HVN was also significant. Conclusions Functional connectivity is an effective noninvasive algorithm, which can help to exploring spontaneous patterns changes in amblyopia. And multiple area existed patterns abnormal and some of them may relate to the functional connectivity. These resultshave important implications for models of amblyopia and approaches to treatment.