The deformation characteristics of Chinese yam during multiphase microwave drying (MMD) was evaluated by image processing, and the effects of MMD on the drying characteristics, physical properties, shrinkage behavior, and microstructure of the samples were also investigated. The drying time was significantly reduced by increasing microwave power density. Compared with Scheme I, the time of Scheme V was shortened by 22.22%. The moisture content at the transition point from sublimation to evaporation drying stages (TPS-E) significantly affected the shrinkage of the samples. In Scheme I, the lowest moisture content at TPS-E of 0.354 g. g−1 was found, and the dried products with the shrinkage ratio and bulk density closest to those of FD. The deformation of Chinese yam mainly appeared in the evaporation drying stage. At this stage, the rate of change in cross-sectional area of dried samples ranged from 9.74% to 26.76% for Schemes II to Scheme V, compared to 2.03% for Scheme I. Similarly, the shrinkage ratio of the dried samples in Schemes II, III, IV, and V increased from 16.82% to 21.12% at TPS-E to 29.23% to 51.28% at the end of drying, respectively. Additionally, the shrinkage caused by the pores collapse of the samples because of the high moisture content at TPS-E (Scheme III, IV, and V) during the evaporation drying stage resulted in increases of bulk density. The present study can provide valuable insights for rational control of shrinkage and deformation of fruits and vegetables in MMD. Industrial relevanceChinese yam is a widely used food and medicinal resource in China due to its rich nutritional and medicinal values. Since the moisture content of Chinese yam can reach as high as 70–80%, drying serves as an effective method to broaden its application. However, shrinkage and deformation of materials during drying are common forms of appearance deterioration that can directly impact consumer acceptability. MMD has proven to be a promising drying technology. Nevertheless, improper drying parameter settings may lead to a deterioration of the appearance quality of MMD products. Therefore, comprehending the information of shrinkage and deformation of Chinese yam during MMD and effectively regulating these processes is essential. Mastering these aspects is critical for enhancing the economic value and consumer acceptance of dried Chinese yam products.