Resting-state functional MRI (RS-fMRI) studies have provided evidences for abnormal intrinsic brain activity in both schizophrenia and Bipolar disorder, but results are inconsistent. We conducted a meta-analysis of whole-brain, RS-fMRI studies to explore the Regional Homogeneity (ReHo) differences between patients with bipolar disorder (BD) and schizophrenia(SCZ). Our results suggested that the brain regions with convergent changes of ReHo in SCZ and BD included the Insular and prefrontalis lobe. While, the occipital lobe showed divergent change, where the ReHo value in SCZ decreases more. Patients with SCZ demonstrated much more widespread brain functional damage, including the decreased ReHo in sensorimotor area.