Foxtail millet （FM） is usually eaten after cooking in daily life， however， studies about the structural and functional properties changes of the main storage protein prolamin in FM before and after cooking are limited. In this study， the prolamins from uncooked and cooked FM were extracted respectively， and the structural and functional changes of which were compared. Scanning electron microscopy results showed that the structure of prolamin from cooked FM was different from that from uncooked FM， as evidenced by occurrence of protein body cross-linking between each other and the changes in protein shape from circular to irregular. The differential scanning calorimetry results further confirmed that the denaturation temperature of prolamin in cooked FM was increased， thus demonstrating that the structure of which tended to be stable. In addition， the amino acid content of prolamin in cooked FM was significantly higher than that in uncooked foxtail millet. Moreover， the secondary structure analysis revealed that part of β-fold was converted to α-helix in prolamin from cooked FM， which indicated that its structure became stable. Furthermore， solubility of prolamin in cooked FM was decreased when compared with prolamin in uncooked FM. Taken together， significant structural and functional changes occurred in FM prolamin after cooking.