BACKGROUND: Major depressive disorder (MDD) and generalized anxiety disorder (GAD) are two of the leading causes of impairment to human mental health. These two psychiatric disorders overlap in many symptoms and neurobiological features thus difficult to distinguish in some cases. METHODS: We enrolled 102 participants, comprising 40 patients with MDD, 32 patients with GAD and 30 matched healthy controls (HCs), to undergo multimodal magnetic resonance imaging (MRI) scans. We identified 18 major white matter (WM) tracts with automated fiber quantification (AFQ) method, to evaluated microstructure with fractional anisotropy (FA) and function with amplitude of low-frequency fluctuation (ALFF). An analysis of variance (ANOVA) was employed to identify differences among groups. We further explored the correlations of FA and ALFF features with clinical symptoms. RESULTS: We identified the white matter microstructure and function of 89 participants. ANOVA and post-hoc analysis revealed that GAD group exhibited significantly higher FA of right anterior thalamic radiation (ATR) than in MDD and HC groups. Additionally, MDD group exhibited significantly decreased ALFF in forceps major (FMA), forceps minor (FMI), bilateral corticospinal tracts (CST) and left inferior fronto-occipital fasciculus (IFOF) compared to both GAD and HC group. ALFF of right CST was significantly negatively correlated to HAMA and a moderate effect size and marginal significance was found between FA of the right ATR and HAMA in GAD group. LIMITATIONS: This study used cross-sectional data and sample size was small. CONCLUSION: Tracking microstructure and function of WM with AFQ method has the potential to distinguish different psychiatric diseases.