Childhood maltreatment has long-term effects on brain structure, inflammation and psychiatric symptoms, yet its impact on white matter (WM) integrity in bipolar disorder type II depression (BDII-D) remains understudied. Here, we investigate WM alterations in BDII-D and their associations with childhood maltreatment, inflammation and psychiatric symptoms. Using TractSeg, we analyzed WM integrity in 146 patients with BDII-D and 151 healthy controls, identifying significantly lower fractional anisotropy (FA) in the corpus callosum, left inferior longitudinal fasciculus and right striato-fronto-orbital tract, alongside higher FA in sensory-motor regions. WM alterations were correlated with inflammatory markers and psychiatric symptoms. Non-negative matrix factorization and clustering analysis revealed two BDII-D subgroups, with one subgroup showing lower corpus callosum FA, higher inflammatory markers, greater childhood emotional maltreatment and psychiatric symptoms. These findings suggest deficits in WM integrity in thalamo-subcortical-cortical and somatosensory areas in BDII-D. Childhood emotional maltreatment may contribute to long-term effects on inflammation and psychiatric symptoms in adulthood BDII-D.