Abstract: The Chenopodium quinoa starch (white Chenopodium quinoa starch WCS, red Chenopodium quinoa starch RCS, black Chenopodium quinoa starch BCS) from Qinghai plateau extracted by alkaline protease were studied based on the changes of amylose and amylopectin contents. The gelatinization treatment was imposed on the three kinds of Chenopodium quinoa starch (the gelatinization temperature was 100℃ and the ratio of material to liquid was 1:12 g/mL).Scanning electron microscope, laser particle size analyzer, X-ray diffractometer, infrared spectrometer, differential scanning calorimeter and other instruments were used to analyze the morphology, crystal structure, molecular structure and thermal properties of Chenopodium quinoa starch. And the differences before and after gelatinization of Chenopodium quinoa starch were compared. The results showed that, the Chenopodium quinoa starch extracted by alkaline protease starch had smooth and complete surface structure by SEM, the surface of the starch granules was highly damaged after gelatinization, the size of starch granules was increased which determined by laser particle size analyzer, the particle size D (10) of the three Chenopodium quinoa starches increased 25.58, 9.16 and 27.00 μm respectively after gelatinization treatment. The X-ray diffraction showed that the starch crystal structure disappeared after gelatinization, and the crystal region changed to amorphous region. The Fourier infrared spectrum results showed that the structure of the three kinds of starch were constant after gelatinization, molecular bonds were not destroyed, only with the increasing of the transmittance. Gelatinization could improve the processing properties of Chenopodium quinoa starch and provide a theoretical basis for the application of Chenopodium quinoa starch.