Isoamylase (Glycogen 6-glucanohydrolase) 
(Flavobacterium odoratum)

Phosphorus, a key trace element, significantly influences starch structure and functionality. However, its specific effects on naked oat starch remain unclear, limiting further development and industrial applications. This study explored the relationship between the chemical composition, molecular structure, and thermodynamic properties of six Chinese naked oat starch varieties extracted via the alkali method, with a particular focus on their phosphorus content. Results showed that all starch samples exhibited A-type crystallinity, irregular polygonal granules, and dense structures, with phosphorus content varying from 416.6 to 904.1 ppm. Crystallinity and thermal analyses revealed substantial differences in starch properties across varieties. Notably, some naked oat starches with higher amylopectin A-chain proportions exhibited elevated relative crystallinity, gelatinization temperatures, and thermal stability due to higher phosphorus content. Pearson correlation analysis revealed positive correlations between phosphorus content and amylopectin B2 (DP 25–36) and B3 (DP > 36) chain proportions, gelatinization enthalpy (r = 0.97, p < 0.05), onset temperature (r = 0.82, p < 0.05) and breakdown viscosity (r = 0.98, p < 0.05), but a negative correlation with peak viscosity (r = −0.62, p < 0.05). The long chains of amylopectin (DP > 24) provide more binding sites and space, facilitating the interaction of phospholipids and the formation of complexes, thereby enhancing crystalline order and thermal stability. Overall, this study elucidates the critical role of phosphorus in modulating naked oat starch structure and thermodynamic behavior, providing valuable insights for the industrial application of starch.