While white matter impairments play an integral part in the pathophysiology of schizophrenia and bipolar disorder, the literature on white matter abnormality differences between the two disorders is insufficient. The University of California Los Angeles Consortium for Neuropsychiatric Phenomic LA5c public dataset, including 47 patients with schizophrenia, 47 with bipolar disorder, and 115 healthy controls, was obtained via OpenNeuro. Whole-brain tractography was performed using Unscented Kalman filter-based two-tensor tractography and White Matter Query Language. Diffusion indices, including fractional anisotropy (FA), axial diffusivity, radial diffusivity (RD), and trace (TR), were used to compare subject groups. Spearman's partial correlation with a covariate of age was used for correlation with clinical variables. Both patient groups exhibited significantly higher RD in the left external capsule and TR in the right extreme capsule. Significantly lower FA in the left external capsule, right thalamo-occipital and thalamo-parietal tracts were found in the schizophrenia group in comparison with bipolar disorder and healthy control groups. Compared with healthy controls, patients with schizophrenia had significantly lower FA in the left-to-right lateral orbitofrontal commissural tract. There were possible associations of the FA and RD of the left external capsule with the anxiety-depression score of the Brief Psychiatric Rating Scale in patients with schizophrenia. The white matter alterations identified in schizophrenia and bipolar disorder may be a neurobiological basis contributing to characterization of the two disorders.