Calcium deficiency is a global public health issue because calcium supplements are consistently inefficient. Although there is a large amount of calcium in bovine bones, its bioactivity is rather low. This study aimed to optimize the extraction process of calcium from bovine bones, develop a Lycium barbarum peptide–calcium chelate (LBP-Ca) preparation method, and evaluate calcium supplementation activity via pharmacodynamics tests. Response surface methodology (RSM) with a Box–Behnken design was used to screen the key parameters of the entire extraction process. The optimal conditions were determined as 1.7 mol/L citric acid, 6 h extraction time, and a material-to-liquid ratio of 1:8. The extracted calcium concentration reached 44 mg/mL. LBP-Ca was made from the extracted calcium and Lycium barbarum peptide. In order to confirm the formation of the chelate, it was characterized by means of UV, FT-IR, particle size, zeta potential, and SEM analysis. The results showed that the group with LBP-Ca exhibited significantly increased serum calcium levels (123.0 ± 24.5 μmol/dL) compared to the other groups in the low-calcium mice test. At the same time, LBP-Ca reduced alkaline phosphatase activity almost to normal levels and improved femur parameters and bone microstructure (higher bone volume fraction and trabecular number and better trabecular connectivity). These results indicate that LBP-Ca has superior bioavailability and bone health-promoting effects, which make it possible to develop highly effective calcium supplements from bovine bones.