Abstract: Microwave freeze drying (MFD) can be the rapid removal of water from vegetables and fruits. The quality of dried products can be almost identical to that of conventional freeze drying (FD). MFD can also be expected to potentially replace the conventional FD, particularly for the low cost. However, the excessive local high temperature can result in the local coking during MFD, which has failed to be effectively controlled until now. The excessive local high temperature has restricted the wide range of applications of MFD. In this study, micro-computed tomography (CT) was used to visualize the pore distribution of dried Chinese yam under different microwave loading levels and cavity pressure. A systematic analysis was implemented to determine the pore size and distribution in every partial specimen. The heat and mass transfer mechanism was given for the uneven distribution of temperature during MFD, even for the excessive local temperature. A series of numerical simulations was then carried out to verify the pore size and pore distribution of the structure model. The results indicated that the operation conditions (such as microwave loading level and cavity pressure) shared a significant effect on the pore characteristics of Chinese yam under MFD. There was a distinct distribution in the thickness of the sarcocarp, as the cavity pressure changed. The percentage of 10-50 μm sarcocarp under 200 Pa was higher than that under 100 and 300 Pa. while the percentage of 60-160 μm sarcocarp under 200 Pa was lower than that under 100 and 300 Pa. Low microwave loading level tended to form the small pores, whereas, the large pores were observed at high microwave loading level. Low cavity pressure and microwave loading levels tended to form the much smaller pores. The low microwave loading level also induced the smaller pores with a size between 50 and 160 μm. Meanwhile, the high microwave loading level tended to produce much larger pores with sizes between 200 and 550 μm. There was a significant effect of cavity pressure on the pore size and distribution in the inner specimen, whereas, there was no effect in the outer specimen. Therefore, the larger pore was more prone to form in the middle of the sample during MFD. There was a distinct effect of microwave loading level on the pore size and distribution in both the inner and outer layers. The microwave loading level was prone to produce sudden variation in the pore distribution when the pore size was larger than 800 μm. Compared with the cavity pressure, the microwave loading level can be more likely to change the pore size and pore distribution from the inside out, where a lot of large pores were formed in the inner specimen with a size of larger than 800 μm. The finding can also offer experimental support to the numerical simulation for the local high temperature in MFD.