Quillaja saponins (QS), a natural amphiphilic food additive, have significant potential in modulating the properties of starchy products. However, a systematic understanding of this phenomenon and the underlying molecular mechanisms remains lacking. In this study, two-stage molecular dynamics (MD) simulations combined with multiple experimental approaches were employed to investigate the modulation of starch properties by QS through six chain dynamic behaviors. The results revealed that the Bola-type structure of QS, characterized by its hydrophobic segment and hydrophilic ends, provides steric hindrance and additional hydrogen bonding sites, which disrupt the formation of interchain hydrogen bonds in starch. This interaction mode facilitated gelatinization (i.e., chain unwinding, pasting temperature: ↓4.1 °C), reduced paste viscosity (i.e., chain movement, ↓60.77 Pa.s), and retarded gelation (i.e., chain rearrangement and short-term reassociation, hardness: ↓5.50 gf) and retrogradation (i.e., long-term chain reassociation, hardening rate: ↓2.23 gf/d). Additionally, QS had minimal effects on starch digestibility (chain depolymerization). This study offers a novel strategy and theoretical basis for the property modulation of starch products.