Microwave energy is widely used in the field of starchy food processing and heating. To date, research on microwave heating has focused predominantly on gelatinization. In order to investigate the mechanism of microwave heating, we selected potato starch, which has a typical B-type crystalline structure of regular shape that is used and consumed widely. Based on the characteristics of the microwave heating process, we established a control heating model and evaluated this with both standard and polarizing light microscopy, laser particle size distribution analysis, and differential scanning calorimetry to probe the destruction of birefringence, the effects on the granule state, and the enthalpy involved. The results showed that thermal-and microwave-specific effects applied to the different stage of gelatinization. Microwave-specific effects dominated initially, but thermal effects began to dominate during and after gelatinization. The starch-water system was affected by microwave radiation throughout the heating process.