The characteristics and quality of Cistanche deserticola (C. deserticola) such as drying rate, color, texture, shrinkage, and microstructure have been investigated under hot air drying (HA), infrared drying (IR), freeze drying (FD), and microwave vacuum freeze drying (MFD). The results showed that the drying rates of C. deserticola were all in the stage of slow-down drying, and there was no obvious constant-speed drying stage under the four different drying methods. Only MFD had the highest drying rate and required 9.6 times less drying time than FD. MFD could obtain the samples that had the most similar color to the fresh sample with the least shrinkage and the greatest hardness and crispness. MFD was similar to FD dried products, with a flat and clear surface and spongy porous structure, but MFD had slightly larger pores than FD. The cell wall structure of IR and HA dried products was damaged and the tissue cells were severely wrinkled; also, the quality characteristics of the products were poor. Through comprehensive analysis, we showed that MFD is a potential drying method that can be used as reference for the production of dried C. deserticola.