The relationship of the hierarchical organization of the skeleton with the local electronic and atomic structure of bone is investigated. The Ca 2p photoemission from intact and various arthritis-damaged areas was measured and examined to study site-dependent peculiarities of calcium bonds in subchondral femoral bone. The medial and lateral condyles of the femur resected during total knee arthroplasty were used as samples. The Ca 2p3/2,1/2–1 photoelectron spectra demonstrate the distinct hierarchy-induced deviations of calcium bonds on the proximal side of the samples. It is shown that the apatite calcium bonds dominate in intact area, whereas non-apatite bonds dominate in OA-damaged areas, especially near sclerotic area but not inside it. The site dependence is associated with the interaction of broken collagen molecules with hydroxyapatite nanocrystallites at the cartilage–bone interface. The interplay of biomechanical and biochemical processes is examined, and the restoration of calcium bonds in sclerotic bone is discussed.