Cross-sex hormones in female-to-male (FtM) transsexuals play a crucial role in brain plasticity. Morphological study associated with white matter (WM) volume in postoperative FtM transsexuals receiving cross-sex hormones has not been published yet. This study was performed to discriminate the regional WM volume differences between postoperative FtM transsexuals and female controls using voxel-based morphometry (VBM) and further to assess the correlations between regional volume variations and cross-sex hormones. WM volume was assessed in 12 postoperative FtM transsexuals receiving cross-sex hormones with 16 age-matched female controls. WM volume was processed using SPM8 software with diffeomorphic anatomical registration via an exponentiated Lie algebra (DARTEL) algorithm. Serum sex hormones, including estriol, free testosterone (free-T), estradiol, follicle-stimulating hormone, and luteinizing hormone were measured. Postoperative FtM transsexuals showed significantly (p < 0.05) larger WM volumes in the inferior parietal lobule, postcentral gyrus, and middle temporal gyrus compared with female controls. However, there were no brain areas with larger WM volume in female controls compared with FtM transsexuals. WM volumes of the inferior parietal lobule and middle temporal gyrus in FtM transsexuals were positively correlated with the levels of free-T. This study revealed WM volume change and its correlation with free-T level in postoperative FtM transsexuals. These findings will improve our understanding of the morphometric changes in FtM transsexuals under cross-sex hormone therapy.