To research functional status of brain regions in migraine patients at different stages by using resting functional magnetic resonance (fMRI), and to explore its relationship with clinical symptoms. Methods: Nineteen active migraine patients were included in the episode group, 22 patients in remission were included in the remission group, and 22 healthy controls were included in the control group. Scanning of all subjects was performed with resting state functional magnetic resonance imaging (rs-fMRI), and post-processing was completed using regional homogeneity (ReHo) analysis. The frequency and duration of migraine were taken as the main clinical observation indexes. The Montreal cognitive assessment scale (MoCA), simple mental state examination (MMSE), Hamilton anxiety scale (HAMA), and Hamilton depression scale (HAMD) were used to measure cognition and neuropsychological state. Results: MoCA score in the episode group was lower than those in the other two groups, while HAMA and HAMD scores in the episode group and remission group were higher than those in the control group (P<0.01). Compared with that of the control group, the ReHo value of the remission group had no significant difference (P>0.05). Compared with that of the control group, the ReHo value in the bilateral lobe, dorsolateral frontal gyrus, cingulate, pars opercularis, insula, left middle frontal gyrus, left anterior cingulate, and amygdala were lower in the episode group (P<0.01). Compared with that of the episode group, the ReHo value in the right limbic lobe, insula, right cingulate gyrus, dorsolateral superior frontal gyrus, caudate nucleus, supplementary motor area, left hippocampus, left frontal lobe, superior temporal gyrus, thalamus, and right middle frontal gyrus were higher in the remission group (P<0.01). The ReHo value of the MIN coordinate (18, －12, 33) brain region (include the insula and cingulate gyrus) was positively correlated with attack frequency and headache duration in migraine patients. Conclusion: Migraines affect mood and cognition. The ReHo values in multiple brain areas in the episode group were weaker than those in the control group and remission group. The MNI coordinate (18, －12, 33) ReHo values were positively correlated with clinical symptoms including the frequency of attack and headache duration, and mainly involved the insula and cingulate gyrus.