The invention relates to a calcium chelating peptide as well as a preparation method and an application thereof. An amino acid sequence of the calcium chelating peptide is FDHIVY. The calcium chelating peptide provided by the invention is safe and non-toxic, and has better physicochemical activity compared with a traditional calcium supplement, and the calcium chelating capability of the calcium chelating peptide reaches 35.73 mg/g; the collagen peptide can be supplemented while absorption and bioavailability of calcium in a human body are improved, the absorption and transport of calcium in Caco-2 small intestinal epithelial cells can be promoted, and the calcium chelating peptide can be used as a raw material for drug development and biological calcium supplementation agents. According to the preparation method provided by the invention, the calcium chelating peptide is successfully obtained, fish product resources can be fully utilized, the operation is simple, and a new way is provided for high-valued utilization of tilapia bones.