Identifying white matter (WM) microstructural similarities and differences between major depressive disorder (MDD) and bipolar disorder (BD) is an important way to understand the potential neuropathological mechanism in emotional disorders. Numerous diffusion tensor imaging (DTI) studies over recent decades have confirmed the presence of WM anomalies in these two affective disorders, but the results were inconsistent. This study aimed to determine the statistical consistency of DTI findings for BD and MDD by using the coordinate-based meta-analysis (CBMA) approach.We performed a systematic search of tract-based spatial statistics (TBSS) studies comparing MDD or BD with healthy controls (HC) as of June 30, 2024. The seed-based d-mapping (SDM) was applied to investigate fractional anisotropy (FA) changes. Meta-regression was then used to analyze the potential correlations between demographics and neuroimaging alterations.Regional FA reductions in the body of the corpus callosum (CC) were identified in both of these two diseases. Besides, MDD patients also exhibited decreased FA in the genu and splenium of the CC, as well as the left anterior thalamic projections (ATP), while BD patients showed FA reduction in the left median network, and cingulum in addition to the CC.The results highlighted that altered integrity in the body of CC served as the shared basis of MDD and BD, and distinct microstructural WM abnormalities also existed, which might induce the various clinical manifestations of these two affective disorders. The study was registered on PROSPERO (http://www.crd.york.ac.uk/PROSPERO), registration number: CRD42022301929.© 2024 The Author(s). Published by IMR Press.