The high comorbidity of major depressive disorder (MDD), anxiety disorders (ANX), and post-traumatic stress disorder (PTSD) complicates the study of their structural neural correlates, particularly in white matter (WM) alterations. Using fractional anisotropy (FA), this meta-analysis aimed to identify both unique and shared WM characteristics for these disorders by comparing them with healthy controls (HC). The aggregated sample size across studies includes 3,661 individuals diagnosed with MDD, ANX, or PTSD and 3,140 HC participants. The whole-brain analysis revealed significant FA reductions in the corpus callosum (CC) across MDD, ANX, and PTSD, suggesting a common neurostructural alteration underlying these disorders. Further pairwise comparisons highlighted disorder-specific differences: MDD patients showed reduced FA in the middle cerebellar peduncles and bilateral superior longitudinal fasciculus II relative to ANX patients and decreased FA in the CC extending to the left anterior thalamic projections (ATPs) when compared with PTSD. In contrast, PTSD patients exhibited reduced FA in the right ATPs compared to HC. No significant FA differences were observed between ANX and PTSD or between ANX and HC. These findings provide evidence for both shared and unique WM alterations in MDD, ANX, and PTSD, reflecting the neural underpinnings of the clinical characteristics that distinguish these disorders.