This study investigates the ability of various wheat germ protein hydrolysates (WGPHs) to bind calcium and characterizes the peptide-calcium complexes. We demonstrate that the amount of Ca bound depended greatly on the type of enzyme, degree of hydrolysis (DH), amino acid composition, and molecular mass distribution of different hydrolysates. The maximum level of Ca bound (67.5 mg·g(-1)) occurred when Alcalase was used to hydrolyze wheat germ protein at a DH of 21.5%. Peptide fragments exhibiting high calcium-binding capacity had molecular mass <2000 Da. The calcium-binding peptides mainly consisted of Glu, Arg, Asp, and Gly, and the level of Ca bound was related to the hydrophobic amino acid content in WGPHs. UV-visible and Fourier transform infrared spectra demonstrate that amino nitrogen atoms and oxygen atoms on the carboxyl group were involved in complexation. Therefore, wheat germ protein is a promising protein source for the production of calcium-binding peptides and could be utilized as a bioactive ingredient for nutraceutical food production.