Objective To explore the difference of white matter changes between bipolar affective disorder and schizophrenia using diffusion tensor imaging (DTI). Methods Patients with bipolar affective disorder and schizophrenia were selected from the Mental Health Center of West China Hospital of Sichuan University between October 2014 and January 2017. Volunteers were recruited from October 2014 to January 2017. The included patients were divided into bipolar affective disorder group and schizophrenia group according to their diagnosis. Volunteers were divided into normal control group. The bipolar affective disorder group was divided into two subgroups: manic episode and depressive episode. DTI was performed on the included patients and volunteers. Tract based spatial statistics (TBSS) was used to study the differences in fractional anisotropy (FA) of white matter between patients and normal controls, and FA values of two subgroups of bipolar affective disorder and schizophrenia were compared. Results A total of 99 patients and 40 normal controls were included in this study. Among them, there were 40 cases in schizophrenia group and 59 cases in bipolar affective disorder group (31 cases of manic episode and 28 cases of depressive episode). Compared with the normal control group, FA values decreased in corpus callosum, fornix, occipital forceps and left inferior longitudinal fasciculus with bipolar affective disorder group and schizophrenia group (P<0.05). There was no significant difference in FA values between bipolar affective disorder group and schizophrenia group (P>0.05), but the FA value in left posterior thalamic radiation decreased in depressive episode of bipolar affective disorder group compared with schizophrenia group (P=0.001). Conclusions There are similarities between white matter changes in bipolar affective disorder and schizophrenia. However, the white matter change in posterior thalamic radiation may be the characteristic change in depressive episode of bipolar affective disorder.