In order to investigate the mechanism of microwave heating, potato starch was selected as the research sample because of its typical B-type crystalline structure. Based on the characteristics of the microwave heating process, a control heating model was established and evaluated. Using 1H NMR technique, Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence and principal component analysis (PCA) to obtain the original transverse relaxation curves of samples that underwent microwave, rapid, and slow heating. The transverse relaxation time (T2) was calculated through multi-exponential regression to analyze the variation patterns of water in the samples in order to study impact of microwave heating on the water state and distribution in potato starch granules. The results showed that there were significant differences in T2 with all three types of heating; microwave heating exerted a particularly significant impact on moisture distribution within the potato starch granules in the early stages of gelatinization. To a certain extent, this study showed that the special effects of microwave accelerated the destruction of hydrogen bonds at this stage.