Background: Migraine, a neurological disorder under perpetual investigation, has an elusive etiology. An potential association with Right-to-Left Shunt (RLS) exists, yet the precise nature of this connection remains unclear.This study employs the resting-state functional magnetic resonance imaging (rs-fMRI) technique to examine brain functional differences between the migraine patients with and without RLS, aiming at exploring RLS associated alterations in functional segregation and integration. Methods: This study included 32 migraine patients (14 patients with RLS and 18 without RLS), each undergoing rs-fMRI data acquisition. The amplitude of low-frequency fluctuation (ALFF) was employed to investigate functional segregation. Functional connectivity (FC) analysis was conducted to explore the functional integration across distinct brain regions. Graph theory-based network analysis was utilized to assess functional networks in migraine patients with RLS. Pearson correlation analysis further explored the relationship between RLS severity and various functional metrics.. Results: Compared with migraine patients without RLS, migraine patients with RLS exhibited a significant increase in the ALFF in the left middle occipital and superior occipital gyrus; As to FC, the reduced connectivity between the left rolandic operculum and the right middle cingulate gyrus was observed in migraine patients with RLS; Based on the brain networks analysis, migraine patients with RLS displayed higher values of the normalized clustering coefficient and greater betweenness centrality in specific regions, including the left precuneus, right insula, and right inferior temporal gyrus. Further, the study found positive correlations between ALFF values in the temporal lobes, thalamus, left middle occipital, and superior occipital gyrus and RLS severity. Conversely, negative correlations emerged between ALFF values in the right inferior frontal gyrus, middle frontal gyrus, and insula and RLS grading. Finally, the study identified a positive correlation between angular gyrus betweenness centrality and RLS severity. Conclusion: RLS-associated brain functional alterations in migraine consisted of local brain regions, connectivity, and networks involved in pain conduction and regulation did exist in migraine with RLS.