Abstract: Microstructural evolution can often dominate the macroscopic shrinkage and deformation of plant-based food materials. It is very essential to clarify the evolution pattern of pore structure during drying, in order to evaluate the microstructural variations in the materials. Taking Chinese yam as a raw material, this study aims to investigate the conversion of the dehydration process during multiphase microwave drying. The samples of Chinese yam were also obtained under different drying schemes (Scheme 1, 2, and 3, i.e., microwave power densities of 0.1, 0.5, and 0.9 W/g). The microwave power density (0.1, 0.5, and 0.9 W/g) was adjusted at the drying stage of the second sublimation (after 90 min of drying, recorded as sublimation-II). X-ray microcomputed tomography (μCT) was used to visualize the internal structure of Chinese yam. The properties of samples were then acquired for the shrinkage ratio, pore structure, and pore size distribution. The results showed that the time required to reach the critical temperature at the phase transition point for the samples in Schemes 1, 2, and 3) was 195, 155, and 145 min, respectively. At the transition point, the sample of Scheme 1 exhibited the lowest water content (26.16%), the highest open pore rate (57.1%), and the highest number of pores. Furthermore, the smallest volume change of the samples was also observed during evaporation drying. Therefore, the lower microwave power density at the sublimation drying stage effectively reduced the moisture content of the sample at the transition point. Additionally, the open pores were formed to minimize the outstanding shrinkage that occurred in the sample. The sample exhibited a greater number of pores and a smaller volume change during evaporation drying. The open porosity in sublimation-II was reduced by 8.02% and 12.16%, respectively, for Schemes 2 and 3. Subsequently, the higher moisture content of the samples resulted in damage to the pore structure during sublimation drying. There was a notable reduction in the porosity of the samples. The pore diameters of the samples exhibited a non-normal distribution in the three drying schemes. An increasing trend of pores with diameters less than 20 μm was also observed in Schemes 1 and 2. In contrast, the tiny pores in the samples of Scheme 3 continued to decrease with drying, while the number of large pores increased. This trend was related to the larger microwave loading. The equivalent diameters of connected pores in the dried samples exhibited a reduction of 3.08%, 8.37%, and 20.04%, respectively, in three drying schemes, compared with the transition point. There was no significant difference (P > 0.05) in the mean diameter and volume of non-connected pores in the samples at the sublimation drying stage among the three drying schemes. In the samples with the higher water content at the transition point (Scheme 2 and 3), the removal of moisture resulted in a significant increase (P < 0.05) in the equivalent diameter of non-connected pores at the evaporation drying stage. The μCT analysis revealed that there were no significant variations in the internal structure of the sample in Scheme 1, the removal of more moisture at the sublimation drying stage was facilitated to form the more robust pore structure inside the samples. There was no impact of water removal on the microstructure of the samples during evaporation drying. These findings can provide empirical evidence and theoretical insights to efficiently process high-quality dehydrated fruits and vegetables by multiphase microwave drying.