Summary Grape seed polypeptide (GSPP) was obtained by liquid fermentation with Bacillus subtilis TK15.015 from waste grape seed pomace. Its chelation ability with calcium ions was excellent. Simulation of in vitro gastrointestinal digestion showed that GSPP and calcium chelate (GSPP‐Ca) slowly released calcium and decreased stomach stimulation. The solubility and transmission rate of GSPP‐Ca after digestion in the gastrointestinal tract for 8 h maintained high levels of 74.4% and 46.4%, respectively, which far exceeded the levels achieved by other calcium supplements. Structural characterisation showed that calcium ions mainly react with binding sites present in peptides such as carboxyl oxygen, hydroxyl oxygen, amino nitrogen and amide bonds. GSPP‐Ca may be a state in which a calcium‐encapsulating complex formed, leaving calcium ions in a soluble state, suggesting its possible use as a high‐quality calcium supplement.