BACKGROUND: Irritable bowel syndrome (IBS) is a brain-gut disorder with high global prevalence, resulting from abnormalities in brain connectivity of the default mode network and aberrant changes in gray matter (GM). However, the findings of previous studies about IBS were divergent. Therefore, we conducted a meta-analysis to identify common functional and structural alterations in IBS patients. METHODS: Altogether, we identified 12 studies involving 194 IBS patients and 230 healthy controls (HCs) from six databases using whole-brain resting state functional connectivity (rs-FC) and voxel-based morphometry. Anisotropic effect-size signed differential mapping (AES-SDM) was used to identify abnormal functional and structural changes as well as the overlap brain regions between dysconnectivity and GM alterations. RESULTS: Findings indicated that, compared with HCs, IBS patients showed abnormal rs-FC in left inferior parietal gyrus, left lingual gyrus, right angular gyrus, right precuneus, right amygdala, right median cingulate cortex, and left hippocampus. Altered GM was detected in the fusiform gyrus, left triangular inferior frontal gyrus (IFG), right superior marginal gyrus, left anterior cingulate gyrus, left rectus, left orbital IFG, right triangular IFG, right putamen, left superior parietal gyrus and right precuneus. Besides, multimodal meta-analysis identified left middle frontal gyrus, left orbital IFG, and right putamen as the overlapped regions. CONCLUSION: Our results confirm that IBS patients have abnormal alterations in rs-FC and GM, and reveal brain regions with both functional and structural alterations. These results may contribute to understanding the underlying pathophysiology of IBS. SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/prospero, identifier CRD42022351342.