Bone tissue has a highly anisotropic microstructure derived from the crystallographic orientation of apatite and the related collagen matrix alignment. Bone is also a highly vascularized tissue; intraosseous vascularization and bone formation are intimately coupled. Meanwhile, the structural relations between intraosseous vascular networks and bone microstructure are as yet unknown, partially due to technical difficulties in visualizing precise intraosseous vasculatures. The aim of this study is to develop a visualization method suitable for the structural analysis of intraosseous vascular networks and to reveal the relations between bone microstructure and the arrangement patterns of intraosseous vasculatures. Three-dimensional vascular networks were successfully visualized, and region-dependent arrangement patterns of blood vessels were clarified using fluorescent dye-conjugated lectin. Interestingly, the anisotropic structural correlation between bone matrix and the vascular system in a region-specific manner was clarified. The obtained results indicate the molecular interactions between the vascular system and bone tissue as a novel contributor for realization of anisotropic bone matrix construct.