The effect of chlorogenic acid (CA) on the dielectric response of lotus seed starch (LS) after microwave treatment, the behavior and digestive characteristics of the resulting starch/chlorogenic acid complex (LS-CA) at different degrees of gelatinization and the inhibition of α-amylase by chlorogenic acid were investigated. The variation in dielectric loss factor, ε″, and dielectric loss tangent, tanδε, of the microwave thermal conversion indicated that LS-CA had a more efficient microwave-energy-to-thermal-energy conversion efficiency than LS. This gelatinized LS-CA to a greater extent at any given temperature between 65 and 85 °C than LS, and it accelerated the degradation of the starch crystalline structure. The greater disruption of the crystal structure decreased the bound water content and increased the thermal stability of LS-CA compared to LS. The simulated in vitro digestion found that the presence of the LS-CA complex improved the slow-digestion property of lotus seed starch by increasing its content of resistant and slowly digested starch. In addition, the release of chlorogenic acid during α-amylase hydrolysis further slowed starch digestion by inhibiting α-amylase activity. These findings provide a foundation for understanding the correlation between the complex behavior and digestive properties of naturally polyphenol-rich, starch-based foods, such as LS, under microwave treatment, which will facilitate the development of starch-based foods with tailored digestion rates, lower final degrees of hydrolysis and glycemic indices.