To evaluate the spontaneous neuronal activities and the changes of brain functional network in patients with vestibular migraine (VM). Three groups including18 patients with VM, 21 patients with migraine without aura (MWoA) and 21 healthy controls (HCs) underwent the scanning of the resting-state fMRI. Covariance analysis and bonferroni multiple comparisons were used to obtain brain regions with significant differences in amplitude of low-frequency fluctuation (ALFF) values. Furthermore, the brain regions with the most significant differences of ALFF values were recognized as a region of interest (ROI) and functional connectivity (FC) analysis was performed in these regions. (1) ALFF: Compared with HCs, patients with VM showed significantly lower ALFF in the right putamen (P < 0.05), and significantly higher ALFF in the right lingual gyrus (P < 0.05). In addition, compared with MWoA patients, patients with VM showed significantly higher ALFF in the right lingual gyrus (P < 0.05). (2) Compared with HCs, VM patients showed significantly higher FC among the cerebellum, the left dorsolateral superior frontal gyrus and the right putamen (P < 0.05) but significantly lower FC among the left median cingulate, paracingulate gyri and the right putamen (P < 0.05). Compared with MWoA patients, VM patients showed significantly higher FC between the cerebellum and the right putamen (P < 0.05) but significantly lower FC among the left median cingulate, paracingulate gyri and the right putamen (P < 0.05). There are functional abnormalities in nociceptive, vestibular and visual cortex regions in patients with VM during the interictal period.