A demineralized bovine bone was hydrolyzed by a specific bone-degrading collagenolytic protease extracted from Bacillus cereus MBL13 (isolated from chopped animal bone wastes) to utilize its collagen in nutraceuticals with high calcium bioavailability. Bovine bone peptide (BBP), a novel oligophosphopeptide with a high calcium binding ability (8.25 mmol/g-protein), was isolated from bovine bone hydrolysates by Chelex 100, ultrafiltration, hydroxyapatite chromatography, gel filtration chromatography, and reverse-phase high performance liquid chromatography. The results showed that demineralization treatment can significantly increase hydrolysis (p < 0.05). The amino acid content of BBP showed that the Asp, Ala, Tyr, and Thr contents were remarkable increments compared to the bone hydrolysates. The molecular mass of BBP was found to be around 3.305 kDa through SDS-PAGE and MALDI-TOF mass spectrometry. FT-IR spectra showed characteristic absorption peaks. Moreover, BBP exhibited higher calcium binding activity than that of casein oligophosphopeptide (CPP). Therefore, this study demonstrated that B. cereus MBL13 collagenolytic protease (BCC) could degrade bovine bone collagen, and prepared oligophosphopeptide could be utilized as a nutraceutical with high calcium-binding activity.