The resolution achievable in vivo by magnetic resonance imaging (MRI) techniques is not sufficient to depict precisely individual trabeculae and, thus, does not permit the quantification of the “true” trabecular bone morphology and topology. Nevertheless, the characterization of the “apparent” trabecular bone network derived from high-resolution MR images (MRIs) and their potential to provide information in addition to bone mineral density (BMD) alone has been established in studies of osteoporosis. The aim of this work was to show the ability of the three-dimensional-line skeleton graph analysis (3D-LSGA) to characterize high-resolution MRIs of trabecular bone structure. Fifteen trabecular bone samples of the distal radius were imaged using the high-resolution MRI (156 × 156 × 300 μm3) and microcomputed tomography (μCT; 34 × 34 × 34 μm3). After thresholding, the 3D skeleton graph of each binary image was obtained. To remove the assimilated-noise branches of the skeleton graph and smooth this skeleton graph before it was analyzed, we defined a smoothing length criterion (lc), such that all “termini” branches having a length lower than lc were removed. Local topological and morphological LSGA measurements were performed from MRIs and μCT images of the same samples. The correlations between these two sets of measurements were dependent on the smoothing criterion lc, reaching R2 = 0.85 for topological measurements and R2 = 0.57–0.64 for morphological measurements. 3D-LSGA technique could be applied to in vivo high-resolution MRIs of trabecular bone structure, giving an indirect characterization of the microtrabecular bone network.