The mandible is a unique bone with a two-layered structure comprising the alveolar area that holds the teeth and the base of the mandible. When teeth are lost, the alveolar area is quickly resorbed, and the internal structure of the mandible changes greatly. Quantitative assessment of changes in the bone microarchitecture that occur with tooth loss is thus imperative. We therefore quantitatively assessed bone mineral density (BMD) and biological apatite (BAp) crystalline orientation in human edentulous mandibles and elucidated the structural characteristics of human edentulous mandibles. Japanese edentulous mandibles were divided into samples with a high and well-rounded alveolar area and thin cortical bone in the alveolar area (α-type), thick cortical bone (β-type), and those with a low and flat alveolar area (γ-type). BMD and BAp crystalline orientation were measured in the alveolar area and base of the mandible of the site corresponding to the first molar (the region of interest). Although BMD did not differ by site, comparisons of the different types revealed that BMD was high in the α-type and low in the β- and γ-types. BAp crystalline orientation in the alveolar area was observed in the vertical direction to the virtual occlusal plane (Y-axis) and buccalingual direction (Z-axis) in the α-type, whereas weak preferential orientation in the mesiodistal direction (X-axis) was observed in the β- and γ-types. BAp crystals in the base of the mandible showed uniaxial preferential alignment along the X-axis in all three sample types (p < 0.05). These findings demonstrate that most of the human edentulous mandible develops long bone-like characteristics with resorption of the alveolar area and that orientation in the alveolar area varies with morphological changes in the alveolar bone.