Millet was treated at 600 MPa for 15 min and 30 min, respectively (millet: water=1∶1 or 1∶2 (w/w). The effects of different treatment conditions on physicochemical and functional properties of millet flour were investigated to provide a theoretical basis for optimizing the quality characteristics of millet powder. The results showed that high hydrostatic pressure (HHP) treatment affected the morphology, particle size, and crystal characteristics of the four different millet powders. The morphology of starch particles in the whole flour changed from a scattered irregular sphere to complex and bonded to block structure with other substances, and the average particle size decreased significantly. The overall particle size shrank, and the crystal structure changed from natural A type to B type. The effect on the microstructure was particularly significant when the ratio of millet to water was 1∶2. The dynamic rheological tests showed that Gʹ and tanδ of millet paste after HHP treatment were higher than those of original powder, and Gʺ was lower than that of original powder. The results showed that HHP treatment could improve the elasticity and viscosity of millet starch, and this technology could be used as an effective physical modification method to improve the physical properties of millet powder.