Calcium binding peptides from Pacific cod (Gadus macrocephalus) bone have attracted attention due to their potential effects on bone health. In this study, calcium binding peptides (CBP) were prepared from Pacific cod bone by trypsin and neutral protease. Ultraviolet spectra, circular dichroism (CD), and Fourier transform infrared spectroscopy (FTIR) revealed that carboxyl and amino groups in CBP could bind to Ca2+, and form the peptide-calcium complex (CBP-Ca). Single-pass intestinal perfusion (SPIP) experiments indicated that the intestinal calcium absorption was significantly enhanced (p < 0.01) in CBP-Ca treated Wistar rats. The anti-osteoporosis activity of CBP-Ca was investigated in the ovariectomized (OVX) Wistar rat model. The administration of CBP-Ca significantly (p < 0.01) improved the calcium bioavailability, trabecular bone structure, bone biomechanical properties, bone mineral density, and bone mineralization degree. CBP-Ca notably (p < 0.01) increased serum calcium, however, it remarkably (p < 0.01) reduced the levels of osteocalcin (OCN), bone alkaline phosphatase (BALP), tartrate-resistant acid phosphatase isoform 5b (TRAP5b), and C-telopeptide of type I collagen (CTX-1) in serum. Results suggested that the cod bone derived CBP could bind with calcium, improve the intestinal calcium absorption, calcium bioavailability, and serum calcium, then reduce the bone turnover rate, and thus ameliorate osteoporosis.