Food Peptide Calcium Chelate was an excellent calcium supplement. The aim of this study was to isolate peptides with high calcium binding activity from a mixture of casein hydrolyzed peptides, to determine their structural characteristics and to verify their function. Firstly, micellar casein was hydrolyzed by a combination of flavor protease and trypsin. Casein hydrolysate peptides (CHP) with high calcium chelating activity were obtained by three purifications and characterized by high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS), mass spectrometry (MS/MS), and fourier transform infrared spectroscopy (FTIR). The results showed that the purified polypeptide (Tyr-Gln-Glu-Pro) had high calcium binding capacity (70.10 ± 4.23 μg/mg). Animal experiments confirmed that YQEP-Ca was effective in improving the bone microarchitecture of rats, and that the low-calcium-content's medium-dose group also had better utilization than the inorganic and unchelated calcium groups. Therefore, the YQEP-Ca obtained in this study provides new clues for the development of various products.