Pure granular amylose (AM) and pure granular amylopectin (waxy) starch (AP) granules have the high nutritional value in food industry. Effects of microwave treatment (400 W/g DW, 1–8 min) on the structure and properties of transgenic AM granules and AP granules were investigated in direct comparison. Microwave treatment, especially during the first 3 min, decreased the molecular weight of molecules in both the AM and the AP samples. The crystallinity of AM starch initially increased from 15.6% to 20.6%, which was associated with the formation of new V_h-type crystals. After that, crystallinity decreased alongside to 11.3% with the complete disruption of B-type crystals. In contrast, the crystallinity of AP starch initially decreased from 18.9% to 10.8% followed by an increase to 20.0%. Upon prolonged treatment of AM granules, the resistant starch and water solubility was significantly increased. Our data demonstrate notable different microwave-dependent reorganization patterns for pure granular AM and AP molecules as native granular systems, which is helpful to the improvement of functionality of these two starches.