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Nine varieties of lotus root (Suining, Xinhe, Zaohua, Zhonghua, L0014, L0013, Cuiyu, L0011, and Zhenzhu) were selected as the research materials to compare their differences in physical, chemical, and starch characteristics before and after boiling, frying, and microwaving. The results showed that Zhenzhu, Xinhe, L0013, Cuiyu, and Zhonghua belong to the crispy lotus root type, while L0011, L0014, Zaohua, and Suining belong to the powdery lotus root type. Furthermore, the nine varieties were characterized for their starch by optical micrograph (OM), polarized micrograph (PM), scanning electron micrograph (SEM), attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR), X-ray diffraction (XRD), carbon-13 cross-polarization/magic angle spinning nuclear magnetic resonance (13C CP/MAS NMR), and differential scanning calorimetry (DSC). The starch granule of powdery lotus root appeared to be larger than that of crispy lotus, and ATR-FTIR studies revealed that the outer layer of starch granules from nine different varieties of lotus root had a highly organized structure. Moreover, XRD and 13C CP/MAS NMR analyses revealed that starch from eight lotus varieties (Suining, Xinhe, Zaohua, Zhonghua, L0014, L0013, Cuiyu, L0011) belong to the A-crystal type, while starch from Zhenzhu belongs to the CA-crystal type. The starch from powdery lotus root exhibited higher crystallinity, as well as increased gelatinization temperature and enthalpy, indicating that its crystal structure was relatively superior compared to that of crispy lotus starch. The short-range order degree, crystallinity, gelatinization temperature, and heat enthalpy of lotus starch decreased after boiling and frying but increased to varying extents after microwaving. Additionally, the heat resistance and stability of starch particles from crispy lotus root were improved after microwave treatment.