This study used tract-based spatial statistics to examine the relationship between post-traumatic amnesia (PTA) and white matter integrity in patients with a traumatic brain injury (TBI). Forty-seven patients with TBI in the chronic stage and 47 age- and sex-matched normal control subjects were recruited to the study. Correlation coefficients were calculated to observe the relationships among the PTA duration, white matter fractional anisotropy (FA) values, and mini-mental state examination (MMSE) results in the patient group. Both before and after Benjamini-Hochberg (BH) corrections, FA values of 46 of the 48 regions of interests of the patient group were lower than those of the control group. The FA values of column and body of fornix, left crus of fornix, left uncinate fasciculus, right hippocampus part of cingulum, left medial lemniscus, right superior cerebellar peduncle, left superior cerebellar peduncle, and left posterior thalamic radiation (after BH correction: the uncinate fasciculus and right hippocampus part of cingulum) in the patient group were negatively correlated with PTA duration. PTA duration was related to the injury severity of eight neural structures, each of which is involved in the cognitive functioning of patients with TBI. Therefore, PTA duration can indicate injury severity of the above neural structures in TBI patients.