This paper's main aim has been to prepare an polypeptide-calcium-zinc chelate from coix seed and to investigate its structure. Bacillus subtilis and Streptococcus thermophilus were used for fermentation of coix seed (CS). Polypeptide from coix seed (CSP) was separated and purified by gel filtration chromatography and reversed-phase high performance liquid chromatography (RP-HPLC). The molecular weight of CSP was detected by Tricine-sodium dodecyl sulfate-polyacrylamide gel (Tricine-SDS-PAGE) electrophoresis. Taking the chelation rate of zinc and calcium as indicators， single factor and response surface methodology were used to determine optimum preparation conditions of coix seed polypeptide-calcium-zinc (CSP-Ca-Zn) chelate. Ultraviolet spectra， fourier infrared and fluorescent light spectra were applied to predict the structure of CSP-Ca-Zn. The results showed that four components were separated by Sephadex G-15. Among them， A3 showed the highest the chelating capacity of calcium and zinc. A3 was separated by RP-HPLC. The purity of CSP was as high as 93.91%， and its molecular mass was around 7.8 ku. The optimal chelate conditions were determined as follows: mass ratio of CSP to Ca-Zn 4.4∶1， mass ratio of calcium to zinc 1∶1， and pH 3.7. Under these conditions， the chelation rates of zinc and calcium were 52.63% and 63.79%， respectively. The principal binding sites of CSP with calcium and zinc were amino nitrogen and carboxylic acid group， and its spatial structure was also changed. This optimal chelate conditions could obtain CSP-Ca-Zn， which has provided technical reference for the development of new products of coix seed peptide and a new idea for food-borne organic calcium and zinc supplements.