Ménière’s disease (MD) is associated with functional reorganization not only in the auditory or sensory cortex but also in other control and cognitive areas. In this study, we examined intranetwork and internetwork connectivity differences between 55 MD patients and 70 healthy controls (HC) in 9 well-defined resting-state networks. Functional connectivity degree was lower in MD compared to HC in 19 brain areas involved in the somatomotor, auditory, ventral attention, default mode, limbic, and deep gray matter networks. In addition, we observed lower intranetwork connectivity in the auditory, ventral attention, and limbic networks, as well as lower internetwork connectivity between the somatomotor and limbic networks, and between the auditory and somatomotor, deep gray matter, and ventral attention networks, and between the deep gray matter and default mode network. Furthermore, we identified 81 pairs of brain areas with significant differences in functional connectivity between MD patients and HC at the edge level. Notably, the left amygdala’s functional connectivity degree was positively correlated with MD’s disease stage, and the ventral attention network’s intranetwork connectivity was positively correlated with the healthy side vestibular ratio. Our findings suggest that these functional network reorganization alterations may serve as potential biomarkers for predicting clinical progression, evaluating disease severity, and gaining a better understanding of MD’s pathophysiology. Large-scale network studies using neuroimaging techniques can provide additional insights into the underlying mechanisms of MD.