Dipeptidyl peptidase-IV (DPP-IV) is a key target for the treatment of type 2 diabetes mellitus. It is possible that peptides that precisely regulate DPP-IV could be released from coix seed prolamins (CSP), but whether this happens has not yet been investigated. We performed the in silico digestion of CSP and predicted the bioactivity, absorption, transport, toxicity, and allergenicity of the resulting peptides. The simulation predicted that 47 non-toxic bioactive peptides would be released. After screening these, we found that 64.58% of them could possess DPP-IV inhibitory activity. The effect of thermal processing on the amino acid composition and structural properties of CSP was determined, and the DPP-IV inhibitory activity of its digestion-derived peptides was also assessed. The results showed that processing could change the flavour of coix seed and the supply of amino acids. After processing, the spatial conformation of CSP changed from ordered to disordered, and the peptide content and the DPP-IV inhibitory activity of its digestion products significantly increased by 19.89–30.91% and 36.84–42.02%, respectively. These results support the hypothesis that processing can change the protein structure and increase the probability that bioactive peptides will be released. They also have important implications for the development of bioactive peptides and the intensive processing of coix seeds.