Microwave freeze-drying (MFD) is a new freeze-drying technique, which differs from single microwave treatment; it involves simultaneous effects of microwave power, time, and the moisture state applied to the materials. In this study, the effects of MFD under various microwave power densities (0.5, 1.0, and 1.5 W/g) on the drying characteristics of Chinese yam slices and the physicochemical, pasting, and thermal properties as well as the starch digestibility of the flour were investigated using conventional hot air drying (HAD) at 50 °C as a control. Compared to HAD, MFD shortened the drying time up to 14.29~35.71%, with a higher drying efficiency at a high microwave power density (1.5 W/g). MFD yam flours provided benefits over HAD products in terms of color, water/oil absorption capacity, and solubility, exhibiting high hot-paste viscosity but low resistant starch content. The content of total starch and free glucose of the yam flour and its iodine blue value were significantly influenced by the drying method and the MFD process parameters (p < 0.05). MFD processing could disrupt the short-range ordered structure of yam starch. Among the MFD flours, samples dried by MFD at 1.5 W/g presented the highest ratio of peak intensity at 1047 and 1022 cm−1 (R1047/1022) value, gelatinization enthalpy, and resistant starch content. These results gave a theoretical foundation for the novel freeze-drying method that MFD applied to foods with a high starch content, enabling the production of a product with the desired quality.