White matter alterations in patients with chronic migraine (CM) have been reported. Traditional Chinese medicine (TCM) syndromes are clinical syndromes proposed by TCM doctors based on long-term clinical observation and classification of the clinical symptoms and signs of CM patients. This study aimed to analyze the whole-brain diffusion tensor imaging (DTI) data of CM patients with different types of TCM syndromes. Sixteen CM patients diagnosed with liver-yang hyperactivity (LH) syndrome and 16 CM patients with qi-blood deficiency (QD) syndrome were recruited in this study. Thirty-one healthy controls (HCs) were also enrolled. All subjects underwent DTI and T1-weighted MRI acquisition. Thirty HCs and 30 CM patients (LH group: n = 15; QD group: n = 15) were included in the final analysis. No significant difference was observed in the DTI indexes between CM patients and HCs, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD). The mean FAs of the left tapetum and the mean MD values for the right medial lemniscus and the right inferior cerebellar peduncle were significantly different in the LH and HC groups. The mean AD values for the right cingulate gyrus and the left uncinate fasciculus, as well as the mean RD for the right inferior cerebellar peduncle and the left tapetum, were also significantly different between these two groups. CM patients with LH and QD syndrome showed altered FA and diffusivity in comparison to healthy controls, suggesting that there may be significant white matter microstructural alterations in these patients.